signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def chords ( chord_labels , intervals , fs , ** kwargs ) :
"""Synthesizes chord labels
Parameters
chord _ labels : list of str
List of chord label strings .
intervals : np . ndarray , shape = ( len ( chord _ labels ) , 2)
Start and end times of each chord label
fs : int
Sampling rate to synthesize at ... | util . validate_intervals ( intervals )
# Convert from labels to chroma
roots , interval_bitmaps , _ = chord . encode_many ( chord_labels )
chromagram = np . array ( [ np . roll ( interval_bitmap , root ) for ( interval_bitmap , root ) in zip ( interval_bitmaps , roots ) ] ) . T
return chroma ( chromagram , intervals ,... |
def readline ( self , timeout = None ) : # timeout is not in use
"""Read data from port and strip escape characters
: param timeout :
: return : Stripped line .""" | fil = self . port . makefile ( )
line = fil . readline ( )
return strip_escape ( line . strip ( ) ) |
def adjust_short_series ( self , timegrid , values ) :
"""Adjust a short time series to a longer timegrid .
Normally , time series data to be read from a external data files
should span ( at least ) the whole initialization time period of a
HydPy project . However , for some variables which are only used
fo... | idxs = [ timegrid [ hydpy . pub . timegrids . init . firstdate ] , timegrid [ hydpy . pub . timegrids . init . lastdate ] ]
valcopy = values
values = numpy . full ( self . seriesshape , self . initinfo [ 0 ] )
len_ = len ( valcopy )
jdxs = [ ]
for idx in idxs :
if idx < 0 :
jdxs . append ( 0 )
elif idx ... |
def version_option ( version = None , * param_decls , ** attrs ) :
"""Adds a ` ` - - version ` ` option which immediately ends the program
printing out the version number . This is implemented as an eager
option that prints the version and exits the program in the callback .
: param version : the version numb... | if version is None :
module = sys . _getframe ( 1 ) . f_globals . get ( '__name__' )
def decorator ( f ) :
prog_name = attrs . pop ( 'prog_name' , None )
message = attrs . pop ( 'message' , '%(prog)s, version %(version)s' )
def callback ( ctx , param , value ) :
if not value or ctx . resilient_p... |
def cli ( ctx , list , fpga ) :
"""Manage FPGA boards .""" | if list :
Resources ( ) . list_boards ( )
elif fpga :
Resources ( ) . list_fpgas ( )
else :
click . secho ( ctx . get_help ( ) ) |
def delete ( method , hmc , uri , uri_parms , logon_required ) :
"""Operation : Delete HBA ( requires DPM mode ) .""" | try :
hba = hmc . lookup_by_uri ( uri )
except KeyError :
raise InvalidResourceError ( method , uri )
partition = hba . manager . parent
cpc = partition . manager . parent
assert cpc . dpm_enabled
check_valid_cpc_status ( method , uri , cpc )
check_partition_status ( method , uri , partition , invalid_statuses ... |
def export_schema_to_dict ( back_references ) :
"""Exports the supported import / export schema to a dictionary""" | databases = [ Database . export_schema ( recursive = True , include_parent_ref = back_references ) ]
clusters = [ DruidCluster . export_schema ( recursive = True , include_parent_ref = back_references ) ]
data = dict ( )
if databases :
data [ DATABASES_KEY ] = databases
if clusters :
data [ DRUID_CLUSTERS_KEY ]... |
def make_stanza ( self ) :
"""Create and return a presence stanza with the current settings .
: return : Presence stanza
: rtype : : class : ` aioxmpp . Presence `""" | stanza = aioxmpp . Presence ( )
self . _state . apply_to_stanza ( stanza )
stanza . status . update ( self . _status )
return stanza |
def get_genus_type_metadata ( self ) :
"""Overrides get _ genus _ type _ metadata of extended object""" | metadata = dict ( self . my_osid_object_form . _genus_type_metadata )
metadata . update ( { 'read_only' : True } )
return Metadata ( ** metadata ) |
def start ( self ) :
'''Starts a server on the port provided in the : class : ` Server ` constructor
in a separate thread
: rtype : Server
: returns : server instance for chaining''' | self . _handler = _create_handler_class ( self . _rules , self . _always_rules )
self . _server = HTTPServer ( ( '' , self . _port ) , self . _handler )
self . _thread = Thread ( target = self . _server . serve_forever , daemon = True )
self . _thread . start ( )
self . running = True
return self |
def _translate_args ( args , desired_locale = None ) :
"""Translates all the translatable elements of the given arguments object .
This method is used for translating the translatable values in method
arguments which include values of tuples or dictionaries .
If the object is not a tuple or a dictionary the o... | if isinstance ( args , tuple ) :
return tuple ( translate ( v , desired_locale ) for v in args )
if isinstance ( args , dict ) :
translated_dict = { }
for ( k , v ) in six . iteritems ( args ) :
translated_v = translate ( v , desired_locale )
translated_dict [ k ] = translated_v
return t... |
def parse ( directive ) :
"""Given a string in the format ` scope : directive ` , or simply ` scope `
or ` directive ` , return a Placement object suitable for passing
back over the websocket API .""" | if not directive : # Handle null case
return None
if isinstance ( directive , ( list , tuple ) ) :
results = [ ]
for d in directive :
results . extend ( parse ( d ) )
return results
if isinstance ( directive , ( dict , client . Placement ) ) : # We ' ve been handed something that we can simply h... |
def find_package_indexes_in_dir ( self , simple_dir ) :
"""Given a directory that contains simple packages indexes , return
a sorted list of normalized package names . This presumes every
directory within is a simple package index directory .""" | packages = sorted ( { # Filter out all of the " non " normalized names here
canonicalize_name ( x ) for x in os . listdir ( simple_dir ) } )
# Package indexes must be in directories , so ignore anything else .
packages = [ x for x in packages if os . path . isdir ( os . path . join ( simple_dir , x ) ) ]
return package... |
def serialize ( self , include_class = True , save_dynamic = False , ** kwargs ) :
"""Serialize Singleton instance to a dictionary .
This behaves identically to HasProperties . serialize , except it also
saves the identifying name in the dictionary as well .""" | json_dict = super ( Singleton , self ) . serialize ( include_class = include_class , save_dynamic = save_dynamic , ** kwargs )
json_dict [ '_singleton_id' ] = self . _singleton_id
return json_dict |
def add_app_template_global ( self , func : Callable , name : Optional [ str ] = None ) -> None :
"""Add an application wide template global .
This is designed to be used on the blueprint directly , and
has the same arguments as
: meth : ` ~ quart . Quart . add _ template _ global ` . An example usage ,
. .... | self . record_once ( lambda state : state . register_template_global ( func , name ) ) |
def encrypt ( self , message , sessionkey = None , ** prefs ) :
"""Encrypt a PGPMessage using this key .
: param message : The message to encrypt .
: type message : : py : obj : ` PGPMessage `
: optional param sessionkey : Provide a session key to use when encrypting something . Default is ` ` None ` ` .
If... | user = prefs . pop ( 'user' , None )
uid = None
if user is not None :
uid = self . get_uid ( user )
else :
uid = next ( iter ( self . userids ) , None )
if uid is None and self . parent is not None :
uid = next ( iter ( self . parent . userids ) , None )
cipher_algo = prefs . pop ( 'cipher' , uid . ... |
def create_output ( out , shape , dtype , mode = 'w+' , suffix = None ) :
"""Return numpy array where image data of shape and dtype can be copied .
The ' out ' parameter may have the following values or types :
None
An empty array of shape and dtype is created and returned .
numpy . ndarray
An existing wr... | if out is None :
return numpy . zeros ( shape , dtype )
if isinstance ( out , str ) and out [ : 6 ] == 'memmap' :
import tempfile
# noqa : delay import
tempdir = out [ 7 : ] if len ( out ) > 7 else None
if suffix is None :
suffix = '.memmap'
with tempfile . NamedTemporaryFile ( dir = tem... |
def make_sources ( comp_key , comp_dict ) :
"""Make dictionary mapping component keys to a source
or set of sources
Parameters
comp _ key : str
Key used to access sources
comp _ dict : dict
Information used to build sources
return ` OrderedDict ` maping comp _ key to ` fermipy . roi _ model . Source `... | srcdict = OrderedDict ( )
try :
comp_info = comp_dict . info
except AttributeError :
comp_info = comp_dict
try :
spectrum = comp_dict . spectrum
except AttributeError :
spectrum = None
model_type = comp_info . model_type
if model_type == 'PointSource' :
srcdict [ comp_key ] = make_point_source ( com... |
def _init_request_logging ( self , app ) :
"""Sets up request logging unless ` ` APPINSIGHTS _ DISABLE _ REQUEST _ LOGGING ` `
is set in the Flask config .
Args :
app ( flask . Flask ) . the Flask application for which to initialize the extension .""" | enabled = not app . config . get ( CONF_DISABLE_REQUEST_LOGGING , False )
if not enabled :
return
self . _requests_middleware = WSGIApplication ( self . _key , app . wsgi_app , telemetry_channel = self . _channel )
app . wsgi_app = self . _requests_middleware |
def _parse_title ( file_path ) :
"""Parse a title from a file name""" | title = file_path
title = title . split ( '/' ) [ - 1 ]
title = '.' . join ( title . split ( '.' ) [ : - 1 ] )
title = ' ' . join ( title . split ( '-' ) )
title = ' ' . join ( [ word . capitalize ( ) for word in title . split ( ' ' ) ] )
return title |
def main_target_usage_requirements ( self , specification , project ) :
"""Returns the use requirement to use when declaraing a main target ,
which are obtained by
- translating all specified property paths , and
- adding project ' s usage requirements
specification : Use - properties explicitly specified f... | assert is_iterable_typed ( specification , basestring )
assert isinstance ( project , ProjectTarget )
project_usage_requirements = project . get ( 'usage-requirements' )
# We don ' t use ' refine - from - user - input ' because I ' m not sure if :
# - removing of parent ' s usage requirements makes sense
# - refining o... |
async def _recover_jobs ( self , agent_addr ) :
"""Recover the jobs sent to a crashed agent""" | for ( client_addr , job_id ) , ( agent , job_msg , _ ) in reversed ( list ( self . _job_running . items ( ) ) ) :
if agent == agent_addr :
await ZMQUtils . send_with_addr ( self . _client_socket , client_addr , BackendJobDone ( job_id , ( "crash" , "Agent restarted" ) , 0.0 , { } , { } , { } , "" , None , N... |
def draw ( self , renderer ) :
"""Draw the children""" | dpi_cor = renderer . points_to_pixels ( 1. )
self . dpi_transform . clear ( )
self . dpi_transform . scale ( dpi_cor , dpi_cor )
for c in self . _children :
c . draw ( renderer )
self . stale = False |
def filesfile_string ( self ) :
"""String with the list of files and prefixes needed to execute ABINIT .""" | lines = [ ]
app = lines . append
app ( self . input_file . path )
# 1 ) Path of the input file
app ( self . output_file . path )
# 2 ) Path of the output file
app ( self . ddb_filepath )
# 3 ) Input derivative database e . g . t13 . ddb . in
app ( self . md_filepath )
# 4 ) Output molecular dynamics e . g . t13 . md
ap... |
def raise_401 ( instance , authenticate , msg = None ) :
"""Abort the current request with a 401 ( Unauthorized ) response code . If
the message is given it ' s output as an error message in the response body
( correctly converted to the requested MIME type ) . Outputs the
WWW - Authenticate header as given b... | instance . response . status = 401
instance . response . headers [ 'WWW-Authenticate' ] = authenticate
if msg :
instance . response . body_raw = { 'error' : msg }
raise ResponseException ( instance . response ) |
def cscore ( args ) :
"""% prog cscore blastfile > cscoreOut
See supplementary info for sea anemone genome paper , C - score formula :
cscore ( A , B ) = score ( A , B ) /
max ( best score for A , best score for B )
A C - score of one is the same as reciprocal best hit ( RBH ) .
Output file will be 3 - co... | from jcvi . utils . cbook import gene_name
p = OptionParser ( cscore . __doc__ )
p . add_option ( "--cutoff" , default = .9999 , type = "float" , help = "Minimum C-score to report [default: %default]" )
p . add_option ( "--pct" , default = False , action = "store_true" , help = "Also include pct as last column [default... |
def remove_all ( self , key ) :
"""Transactional implementation of : func : ` MultiMap . remove _ all ( key )
< hazelcast . proxy . multi _ map . MultiMap . remove _ all > `
: param key : ( object ) , the key of the entries to remove .
: return : ( list ) , the collection of the values associated with the key... | check_not_none ( key , "key can't be none" )
return self . _encode_invoke ( transactional_multi_map_remove_codec , key = self . _to_data ( key ) ) |
def simxReadVisionSensor ( clientID , sensorHandle , operationMode ) :
'''Please have a look at the function description / documentation in the V - REP user manual''' | detectionState = ct . c_ubyte ( )
auxValues = ct . POINTER ( ct . c_float ) ( )
auxValuesCount = ct . POINTER ( ct . c_int ) ( )
ret = c_ReadVisionSensor ( clientID , sensorHandle , ct . byref ( detectionState ) , ct . byref ( auxValues ) , ct . byref ( auxValuesCount ) , operationMode )
auxValues2 = [ ]
if ret == 0 :
... |
def add_integer_proxy_for ( self , label : str , shape : Collection [ int ] = None ) -> Vertex :
"""Creates a proxy vertex for the given label and adds to the sequence item""" | if shape is None :
return Vertex . _from_java_vertex ( self . unwrap ( ) . addIntegerProxyFor ( _VertexLabel ( label ) . unwrap ( ) ) )
else :
return Vertex . _from_java_vertex ( self . unwrap ( ) . addIntegerProxyFor ( _VertexLabel ( label ) . unwrap ( ) , shape ) ) |
def start ( self , wait = 60 , * , server_settings = { } , ** opts ) :
"""Start the cluster .""" | status = self . get_status ( )
if status == 'running' :
return
elif status == 'not-initialized' :
raise ClusterError ( 'cluster in {!r} has not been initialized' . format ( self . _data_dir ) )
port = opts . pop ( 'port' , None )
if port == 'dynamic' :
port = find_available_port ( )
extra_args = [ '--{}={}'... |
def _inherit_outputs ( self , pipeline_name , already_defined , resolve_outputs = False ) :
"""Inherits outputs from a calling Pipeline .
Args :
pipeline _ name : The Pipeline class name ( used for debugging ) .
already _ defined : Maps output name to stringified db . Key ( of _ SlotRecords )
of any exiting... | for name , slot_key in already_defined . iteritems ( ) :
if not isinstance ( slot_key , db . Key ) :
slot_key = db . Key ( slot_key )
slot = self . _output_dict . get ( name )
if slot is None :
if self . _strict :
raise UnexpectedPipelineError ( 'Inherited output named "%s" must ... |
def _share_project ( self , destination , project , to_user , force_send , auth_role = '' , user_message = '' , share_users = None ) :
"""Send message to remote service to email / share project with to _ user .
: param destination : str which type of sharing we are doing ( SHARE _ DESTINATION or DELIVER _ DESTINA... | from_user = self . remote_store . get_current_user ( )
share_user_ids = None
if share_users :
share_user_ids = [ share_user . id for share_user in share_users ]
item = D4S2Item ( destination = destination , from_user_id = from_user . id , to_user_id = to_user . id , project_id = project . id , project_name = projec... |
def get_code_num_rgb ( s : str ) -> Optional [ Tuple [ int , int , int ] ] :
"""Get rgb code numbers from an RGB escape code .
Raises InvalidRgbEscapeCode if an invalid number is found .""" | parts = s . split ( ';' )
if len ( parts ) != 5 :
raise InvalidRgbEscapeCode ( s , reason = 'Count is off.' )
rgbparts = parts [ - 3 : ]
if not rgbparts [ 2 ] . endswith ( 'm' ) :
raise InvalidRgbEscapeCode ( s , reason = 'Missing \'m\' on the end.' )
rgbparts [ 2 ] = rgbparts [ 2 ] . rstrip ( 'm' )
try :
r... |
def save ( self , * args , ** kwargs ) :
"""Save the person model so it updates his / her number of board connections field .
Also updates name""" | self . name = str ( self . company . name ) + " --- " + str ( self . person )
super ( Director , self ) . save ( * args , ** kwargs )
# Call the " real " save ( ) method .
other_directors = Director . objects . filter ( company = self . company )
for director in other_directors :
director . person . save ( ) |
def _update_in_hdx ( self , object_type , id_field_name , file_to_upload = None , ** kwargs ) : # type : ( str , str , Optional [ str ] , Any ) - > None
"""Helper method to check if HDX object exists in HDX and if so , update it
Args :
object _ type ( str ) : Description of HDX object type ( for messages )
id... | self . _check_load_existing_object ( object_type , id_field_name )
# We load an existing object even thought it may well have been loaded already
# to prevent an admittedly unlikely race condition where someone has updated
# the object in the intervening time
self . _merge_hdx_update ( object_type , id_field_name , fil... |
def run ( self , writer , reader ) :
"""Pager entry point .
In interactive mode ( terminal is a tty ) , run until
` ` process _ keystroke ( ) ` ` detects quit keystroke ( ' q ' ) . In
non - interactive mode , exit after displaying all unicode points .
: param writer : callable writes to output stream , rece... | self . _page_data = self . initialize_page_data ( )
self . _set_lastpage ( )
if not self . term . is_a_tty :
self . _run_notty ( writer )
else :
self . _run_tty ( writer , reader ) |
def unindex_objects ( mapping_type , ids , es = None , index = None ) :
"""Remove documents of a specified mapping _ type from the index .
This allows for asynchronous deleting .
If a mapping _ type extends Indexable , you can add a ` ` pre _ delete ` `
hook for the model that it ' s based on like this : :
... | if settings . ES_DISABLED :
return
for id_ in ids :
mapping_type . unindex ( id_ , es = es , index = index ) |
def get_slice_nodes ( self , time_slice = 0 ) :
"""Returns the nodes present in a particular timeslice
Parameters
time _ slice : int
The timeslice should be a positive value greater than or equal to zero
Examples
> > > from pgmpy . models import DynamicBayesianNetwork as DBN
> > > dbn = DBN ( )
> > > ... | if not isinstance ( time_slice , int ) or time_slice < 0 :
raise ValueError ( "The timeslice should be a positive value greater than or equal to zero" )
return [ ( node , time_slice ) for node in self . _nodes ( ) ] |
def iter_cols ( self , start = None , end = None ) :
"""Iterate each of the Region cols in this region""" | start = start or 0
end = end or self . ncols
for i in range ( start , end ) :
yield self . iloc [ : , i ] |
def stencil_grid ( S , grid , dtype = None , format = None ) :
"""Construct a sparse matrix form a local matrix stencil .
Parameters
S : ndarray
matrix stencil stored in N - d array
grid : tuple
tuple containing the N grid dimensions
dtype :
data type of the result
format : string
sparse matrix fo... | S = np . asarray ( S , dtype = dtype )
grid = tuple ( grid )
if not ( np . asarray ( S . shape ) % 2 == 1 ) . all ( ) :
raise ValueError ( 'all stencil dimensions must be odd' )
if len ( grid ) != np . ndim ( S ) :
raise ValueError ( 'stencil dimension must equal number of grid\
dimens... |
def magic ( adata , name_list = None , k = 10 , a = 15 , t = 'auto' , n_pca = 100 , knn_dist = 'euclidean' , random_state = None , n_jobs = None , verbose = False , copy = None , ** kwargs ) :
"""Markov Affinity - based Graph Imputation of Cells ( MAGIC ) API [ vanDijk18 ] _ .
MAGIC is an algorithm for denoising ... | try :
from magic import MAGIC
except ImportError :
raise ImportError ( 'Please install magic package via `pip install --user ' 'git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python`' )
logg . info ( 'computing PHATE' , r = True )
needs_copy = not ( name_list is None or ( isinstance ( name_list , s... |
async def create_http_connection ( loop , protocol_factory , host , port = 25105 , auth = None ) :
"""Create an HTTP session used to connect to the Insteon Hub .""" | protocol = protocol_factory ( )
transport = HttpTransport ( loop , protocol , host , port , auth )
_LOGGER . debug ( "create_http_connection Finished creating connection" )
return ( transport , protocol ) |
def _read2 ( self , length = None , use_compression = None , project = None , ** kwargs ) :
''': param length : Maximum number of bytes to be read
: type length : integer
: param project : project to use as context for this download ( may affect
which billing account is billed for this download ) . If specifi... | if self . _file_length == None :
desc = self . describe ( ** kwargs )
if desc [ "state" ] != "closed" :
raise DXFileError ( "Cannot read from file until it is in the closed state" )
self . _file_length = int ( desc [ "size" ] )
# If running on a worker , wait for the first file download chunk
# to c... |
def get_qualifier_id ( self ) :
"""Gets the ` ` Qualifier Id ` ` for this authorization .
return : ( osid . id . Id ) - the qualifier ` ` Id ` `
* compliance : mandatory - - This method must be implemented . *""" | # Implemented from template for osid . learning . Activity . get _ objective _ id
if not bool ( self . _my_map [ 'qualifierId' ] ) :
raise errors . IllegalState ( 'qualifier empty' )
return Id ( self . _my_map [ 'qualifierId' ] ) |
def report ( data ) :
"""Create a Rmd report for small RNAseq analysis""" | work_dir = dd . get_work_dir ( data [ 0 ] [ 0 ] )
out_dir = op . join ( work_dir , "report" )
safe_makedir ( out_dir )
summary_file = op . join ( out_dir , "summary.csv" )
with file_transaction ( summary_file ) as out_tx :
with open ( out_tx , 'w' ) as out_handle :
out_handle . write ( "sample_id,%s\n" % _g... |
def _create_connection ( self ) :
"""Create a new websocket connection with proper headers .""" | logging . debug ( "Initializing new websocket connection." )
headers = { 'Authorization' : self . service . _get_bearer_token ( ) , 'Predix-Zone-Id' : self . ingest_zone_id , 'Content-Type' : 'application/json' , }
url = self . ingest_uri
logging . debug ( "URL=" + str ( url ) )
logging . debug ( "HEADERS=" + str ( hea... |
def get_tagged_version_numbers ( series = 'stable' ) :
"""Retrieve git tags and find version numbers for a release series
series - ' stable ' , ' oldstable ' , or ' testing '""" | releases = [ ]
if series == 'testing' : # Testing releases always have a hyphen after the version number :
tag_regex = re . compile ( '^refs/tags/cassandra-([0-9]+\.[0-9]+\.[0-9]+-.*$)' )
else : # Stable and oldstable releases are just a number :
tag_regex = re . compile ( '^refs/tags/cassandra-([0-9]+\.[0-9]+\... |
def detach ( self , dwProcessId , bIgnoreExceptions = False ) :
"""Detaches from a process currently being debugged .
@ note : On Windows 2000 and below the process is killed .
@ see : L { attach } , L { detach _ from _ all }
@ type dwProcessId : int
@ param dwProcessId : Global ID of a process to detach fr... | # Keep a reference to the process . We ' ll need it later .
try :
aProcess = self . system . get_process ( dwProcessId )
except KeyError :
aProcess = Process ( dwProcessId )
# Determine if there is support for detaching .
# This check should only fail on Windows 2000 and older .
try :
win32 . DebugActivePro... |
def check_plugin ( self , plugin ) :
"""Check if the section is in the proper format vcf format .
Args :
vcf _ section ( dict ) : The information from a vcf section
Returns :
True is it is in the proper format""" | vcf_section = self [ plugin ]
try :
vcf_field = vcf_section [ 'field' ]
if not vcf_field in self . vcf_columns :
raise ValidateError ( "field has to be in {0}\n" "Wrong field name in plugin: {1}" . format ( self . vcf_columns , plugin ) )
if vcf_field == 'INFO' :
try :
info_key =... |
def _fetchall ( self , query , vars , limit = None , offset = 0 ) :
"""Return multiple rows .""" | if limit is None :
limit = current_app . config [ 'DEFAULT_PAGE_SIZE' ]
query += ' LIMIT %s OFFSET %s' '' % ( limit , offset )
cursor = self . get_db ( ) . cursor ( )
self . _log ( cursor , query , vars )
cursor . execute ( query , vars )
return cursor . fetchall ( ) |
def show_events ( self , status = None , nids = None ) :
"""Print the Abinit events ( ERRORS , WARNIING , COMMENTS ) to stdout
Args :
status : if not None , only the tasks with this status are select
nids : optional list of node identifiers used to filter the tasks .""" | nrows , ncols = get_terminal_size ( )
for task in self . iflat_tasks ( status = status , nids = nids ) :
report = task . get_event_report ( )
if report :
print ( make_banner ( str ( task ) , width = ncols , mark = "=" ) )
print ( report ) |
def _get_installed ( self ) :
"""Gets a list of the file paths to repo settings files that are
being monitored by the CI server .""" | from utility import get_json
# This is a little tricky because the data file doesn ' t just have a list
# of installed servers . It also manages the script ' s database that tracks
# the user ' s interactions with it .
fulldata = get_json ( self . instpath , { } )
if "installed" in fulldata :
return fulldata [ "ins... |
def digicam_configure_send ( self , target_system , target_component , mode , shutter_speed , aperture , iso , exposure_type , command_id , engine_cut_off , extra_param , extra_value , force_mavlink1 = False ) :
'''Configure on - board Camera Control System .
target _ system : System ID ( uint8 _ t )
target _ c... | return self . send ( self . digicam_configure_encode ( target_system , target_component , mode , shutter_speed , aperture , iso , exposure_type , command_id , engine_cut_off , extra_param , extra_value ) , force_mavlink1 = force_mavlink1 ) |
def _find_export ( self , func ) : # type : ( Callable [ [ Tuple [ Any , EndpointDescription ] ] , bool ] ) - > Optional [ Tuple [ Any , EndpointDescription ] ]
"""Look for an export using the given lookup method
The lookup method must accept a single parameter , which is a tuple
containing a service instance a... | with self . _exported_instances_lock :
for val in self . _exported_services . values ( ) :
if func ( val ) :
return val
return None |
def highlight ( __text : str , * , lexer : str = 'diff' , formatter : str = 'terminal' ) -> str :
"""Highlight text highlighted using ` ` pygments ` ` .
Returns text untouched if colour output is not enabled .
See also : : pypi : ` Pygments `
Args :
_ _ text : Text to highlight
lexer : Jinja lexer to use ... | if sys . stdout . isatty ( ) :
lexer = get_lexer_by_name ( lexer )
formatter = get_formatter_by_name ( formatter )
__text = pyg_highlight ( __text , lexer , formatter )
return __text |
def start ( queue , profile = None , tag = 'salt/engine/sqs' , owner_acct_id = None ) :
'''Listen to sqs and fire message on event bus''' | if __opts__ . get ( '__role' ) == 'master' :
fire_master = salt . utils . event . get_master_event ( __opts__ , __opts__ [ 'sock_dir' ] , listen = False ) . fire_event
else :
fire_master = __salt__ [ 'event.send' ]
message_format = __opts__ . get ( 'sqs.message_format' , None )
sqs = _get_sqs_conn ( profile )
q... |
def access_elementusers ( self , elementuser_id , access_id = None , tenant_id = None , api_version = "v2.0" ) :
"""Get all accesses for a particular user
* * Parameters : * * :
- * * elementuser _ id * * : Element User ID
- * * access _ id * * : ( optional ) Access ID
- * * tenant _ id * * : Tenant ID
- ... | if tenant_id is None and self . _parent_class . tenant_id : # Pull tenant _ id from parent namespace cache .
tenant_id = self . _parent_class . tenant_id
elif not tenant_id : # No value for tenant _ id .
raise TypeError ( "tenant_id is required but not set or cached." )
cur_ctlr = self . _parent_class . control... |
def go_to_line ( self , line = None ) :
"""Go to line dialog""" | if line is not None : # When this method is called from the flileswitcher , a line
# number is specified , so there is no need for the dialog .
self . get_current_editor ( ) . go_to_line ( line )
else :
if self . data :
self . get_current_editor ( ) . exec_gotolinedialog ( ) |
def _newIdentifier ( self ) :
"""Make a new identifier for an as - yet uncreated model object .
@ rtype : C { int }""" | id = self . _allocateID ( )
self . _idsToObjects [ id ] = self . _NO_OBJECT_MARKER
self . _lastValues [ id ] = None
return id |
def requires_list ( self ) :
"""It is important that this property is calculated lazily . Getting the
' requires ' attribute may trigger a package load , which may be avoided if
this variant is reduced away before that happens .""" | requires = self . variant . get_requires ( build_requires = self . building )
reqlist = RequirementList ( requires )
if reqlist . conflict :
raise ResolveError ( "The package %s has an internal requirements conflict: %s" % ( str ( self ) , str ( reqlist ) ) )
return reqlist |
async def create ( source_id : str , attrs : dict , cred_def_handle : int , name : str , price : str ) :
"""Creates a Class representing an Issuer Credential
: param source _ id : Tag associated by user of sdk
: param attrs : attributes that will form the credential
: param cred _ def _ handle : Handle from p... | constructor_params = ( source_id , attrs , cred_def_handle , name , price )
c_source_id = c_char_p ( source_id . encode ( 'utf-8' ) )
c_cred_def_handle = c_uint32 ( cred_def_handle )
c_price = c_char_p ( price . encode ( 'utf-8' ) )
# default institution _ did in config is used as issuer _ did
c_issuer_did = None
c_dat... |
def _send_string_selection ( self , string : str ) :
"""Use the mouse selection clipboard to send a string .""" | backup = self . clipboard . selection
# Keep a backup of current content , to restore the original afterwards .
if backup is None :
logger . warning ( "Tried to backup the X PRIMARY selection content, but got None instead of a string." )
self . clipboard . selection = string
self . __enqueue ( self . _paste_using_m... |
def create_q ( token ) :
"""Creates the Q ( ) object .""" | meta = getattr ( token , 'meta' , None )
query = getattr ( token , 'query' , '' )
wildcards = None
if isinstance ( query , six . string_types ) : # Unicode - > Quoted string
search = query
else : # List - > No quoted string ( possible wildcards )
if len ( query ) == 1 :
search = query [ 0 ]
elif len... |
def _filter ( self , query , ** kwargs ) :
"""Filter a query with user - supplied arguments .""" | query = self . _auto_filter ( query , ** kwargs )
return query |
def drawPoint ( self , x , y , silent = True ) :
"""Draws a point on the current : py : class : ` Layer ` with the current : py : class : ` Brush ` .
Coordinates are relative to the original layer size WITHOUT downsampling applied .
: param x1 : Point X coordinate .
: param y1 : Point Y coordinate .
: rtype... | start = time . time ( )
# Downsample the coordinates
x = int ( x / config . DOWNSAMPLING )
y = int ( y / config . DOWNSAMPLING )
# Apply the dab with or without source caching
if self . brush . usesSourceCaching :
applyMirroredDab_jit ( self . mirrorMode , self . image . getActiveLayer ( ) . data , int ( x - self .... |
def _draw_fold_indicator ( self , top , mouse_over , collapsed , painter ) :
"""Draw the fold indicator / trigger ( arrow ) .
: param top : Top position
: param mouse _ over : Whether the mouse is over the indicator
: param collapsed : Whether the trigger is collapsed or not .
: param painter : QPainter""" | rect = QRect ( 0 , top , self . sizeHint ( ) . width ( ) , self . sizeHint ( ) . height ( ) )
if self . _native_icons :
opt = QStyleOptionViewItem ( )
opt . rect = rect
opt . state = ( QStyle . State_Active | QStyle . State_Item | QStyle . State_Children )
if not collapsed :
opt . state |= QStyl... |
def as_dot ( self ) -> str :
"""Return as a string the dot version of the graph .""" | return nx . drawing . nx_pydot . to_pydot ( self . _graph ) . to_string ( ) |
def _cont_norm_running_quantile_mp ( wl , fluxes , ivars , q , delta_lambda , n_proc = 2 , verbose = False ) :
"""The same as _ cont _ norm _ running _ quantile ( ) above ,
but using multi - processing .
Bo Zhang ( NAOC )""" | nStar = fluxes . shape [ 0 ]
# start mp . Pool
mp_results = [ ]
pool = mp . Pool ( processes = n_proc )
for i in xrange ( nStar ) :
mp_results . append ( pool . apply_async ( _find_cont_running_quantile , ( wl , fluxes [ i , : ] . reshape ( ( 1 , - 1 ) ) , ivars [ i , : ] . reshape ( ( 1 , - 1 ) ) , q , delta_lambd... |
def Logout ( self , dumpXml = None ) :
"""Logout method disconnects from UCS .""" | from UcsBase import UcsException
if ( self . _cookie == None ) :
return True
if self . _refreshTimer :
self . _refreshTimer . cancel ( )
response = self . AaaLogout ( dumpXml )
self . _cookie = None
self . _lastUpdateTime = str ( time . asctime ( ) )
self . _domains = None
self . _priv = None
self . _sessionId ... |
def SortBy ( * qs ) :
"""Convert a list of Q objects into list of sort instructions""" | sort = [ ]
for q in qs :
if q . _path . endswith ( '.desc' ) :
sort . append ( ( q . _path [ : - 5 ] , DESCENDING ) )
else :
sort . append ( ( q . _path , ASCENDING ) )
return sort |
def plugin_for ( cls , model ) :
'''Find and return a plugin for this model . Uses inheritance to find a model where the plugin is registered .''' | logger . debug ( "Getting a plugin for: %s" , model )
if not issubclass ( model , Model ) :
return
if model in cls . plugins :
return cls . plugins [ model ]
for b in model . __bases__ :
p = cls . plugin_for ( b )
if p :
return p |
def compress_ranges_to_lists ( self ) :
'''Converts the internal dimension ranges on lists into
list of the restricted size . Thus all dimension rules
are applied to all dimensions of the list wrapper
and returned as a list ( of lists ) .''' | clist = [ ]
for elem in self :
if isinstance ( elem , FixedListSubset ) :
clist . append ( elem . compress_ranges_to_lists ( ) )
else :
clist . append ( elem )
return clist |
def draw_light_2d_linear ( self , kwargs_list , n = 1 , new_compute = False , r_eff = 1. ) :
"""constructs the CDF and draws from it random realizations of projected radii R
: param kwargs _ list :
: return :""" | if not hasattr ( self , '_light_cdf' ) or new_compute is True :
r_array = np . linspace ( self . _min_interpolate , self . _max_interpolate , self . _interp_grid_num )
cum_sum = np . zeros_like ( r_array )
sum = 0
for i , r in enumerate ( r_array ) :
if i == 0 :
cum_sum [ i ] = 0
... |
def insertBefore ( self , newchild , refchild ) :
"""Insert a new child node before an existing child . It must
be the case that refchild is a child of this node ; if not ,
ValueError is raised . newchild is returned .""" | for i , childNode in enumerate ( self . childNodes ) :
if childNode is refchild :
self . childNodes . insert ( i , newchild )
newchild . parentNode = self
self . _verifyChildren ( i )
return newchild
raise ValueError ( refchild ) |
def connect ( self , keyfile = None ) :
"""Connect to the node via ssh using the paramiko library .
: return : : py : class : ` paramiko . SSHClient ` - ssh connection or None on
failure""" | ssh = paramiko . SSHClient ( )
ssh . set_missing_host_key_policy ( paramiko . AutoAddPolicy ( ) )
if keyfile and os . path . exists ( keyfile ) :
ssh . load_host_keys ( keyfile )
# Try connecting using the ` preferred _ ip ` , if
# present . Otherwise , try all of them and set ` preferred _ ip `
# using the first t... |
def _process_diseases ( self , limit = None ) :
"""This method processes the KEGG disease IDs .
Triples created :
< disease _ id > is a class
< disease _ id > rdfs : label < disease _ name >
: param limit :
: return :""" | LOG . info ( "Processing diseases" )
if self . test_mode :
graph = self . testgraph
else :
graph = self . graph
line_counter = 0
model = Model ( graph )
raw = '/' . join ( ( self . rawdir , self . files [ 'disease' ] [ 'file' ] ) )
with open ( raw , 'r' , encoding = "iso-8859-1" ) as csvfile :
filereader = ... |
def append_text ( self , txt ) :
"""adds a line of text to a file""" | with open ( self . fullname , "a" ) as myfile :
myfile . write ( txt ) |
def generic_request ( self , method , uri , all_pages = False , data_key = None , no_data = False , do_not_process = False , force_urlencode_data = False , data = None , params = None , files = None , single_item = False ) :
"""Generic Canvas Request Method .""" | if not uri . startswith ( 'http' ) :
uri = self . uri_for ( uri )
if force_urlencode_data is True :
uri += '?' + urllib . urlencode ( data )
assert method in [ 'GET' , 'POST' , 'PUT' , 'DELETE' , 'HEAD' , 'OPTIONS' ]
if method == 'GET' :
response = self . session . get ( uri , params = params )
elif method ... |
def delete_collection_csi_driver ( self , ** kwargs ) :
"""delete collection of CSIDriver
This method makes a synchronous HTTP request by default . To make an
asynchronous HTTP request , please pass async _ req = True
> > > thread = api . delete _ collection _ csi _ driver ( async _ req = True )
> > > resul... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'async_req' ) :
return self . delete_collection_csi_driver_with_http_info ( ** kwargs )
else :
( data ) = self . delete_collection_csi_driver_with_http_info ( ** kwargs )
return data |
def run_rep ( self , params , rep ) :
"""run a single repetition including directory creation , log files , etc .""" | try :
name = params [ 'name' ]
fullpath = os . path . join ( params [ 'path' ] , params [ 'name' ] )
logname = os . path . join ( fullpath , '%i.log' % rep )
# check if repetition exists and has been completed
restore = 0
if os . path . exists ( logname ) :
logfile = open ( logname , 'r'... |
def destroy ( vm_name , call = None ) :
'''Call ' destroy ' on the instance . Can be called with " - a destroy " or - d
CLI Example :
. . code - block : : bash
salt - cloud - a destroy myinstance1 myinstance2 . . .
salt - cloud - d myinstance1 myinstance2 . . .''' | if call and call != 'action' :
raise SaltCloudSystemExit ( 'The destroy action must be called with -d or "-a destroy".' )
conn = get_conn ( )
try :
node = conn . ex_get_node ( vm_name )
except Exception as exc : # pylint : disable = W0703
log . error ( 'Could not locate instance %s\n\n' 'The following excep... |
def get_word_break_property ( value , is_bytes = False ) :
"""Get ` WORD BREAK ` property .""" | obj = unidata . ascii_word_break if is_bytes else unidata . unicode_word_break
if value . startswith ( '^' ) :
negated = value [ 1 : ]
value = '^' + unidata . unicode_alias [ 'wordbreak' ] . get ( negated , negated )
else :
value = unidata . unicode_alias [ 'wordbreak' ] . get ( value , value )
return obj [... |
def dbStore ( self , typ , py_value ) :
"""Prepares to store this column for the a particular backend database .
: param backend : < orb . Database >
: param py _ value : < variant >
: param context : < orb . Context >
: return : < variant >""" | # convert base types to work in the database
if isinstance ( py_value , ( list , tuple , set ) ) :
py_value = tuple ( ( self . dbStore ( x ) for x in py_value ) )
elif isinstance ( py_value , orb . Collection ) :
py_value = py_value . ids ( )
elif isinstance ( py_value , orb . Model ) :
py_value = py_value ... |
def move ( self , x , y ) :
"""Move window top - left corner to position""" | SetWindowPos ( self . _hwnd , None , x , y , 0 , 0 , SWP_NOSIZE ) |
def tune ( self , verbose = None ) :
"""Tuning initial slice width parameter""" | if not self . _tune :
return False
else :
self . w_tune . append ( abs ( self . stochastic . last_value - self . stochastic . value ) )
self . w = 2 * ( sum ( self . w_tune ) / len ( self . w_tune ) )
return True |
def from_ ( self , selectable ) :
"""Adds a table to the query . This function can only be called once and will raise an AttributeError if called a
second time .
: param selectable :
Type : ` ` Table ` ` , ` ` Query ` ` , or ` ` str ` `
When a ` ` str ` ` is passed , a table with the name matching the ` ` s... | self . _from . append ( Table ( selectable ) if isinstance ( selectable , str ) else selectable )
if isinstance ( selectable , ( QueryBuilder , _UnionQuery ) ) and selectable . alias is None :
if isinstance ( selectable , QueryBuilder ) :
sub_query_count = selectable . _subquery_count
else :
sub... |
def skip_count ( self ) :
"""Amount of skipped test cases in this list .
: return : integer""" | return len ( [ i for i , result in enumerate ( self . data ) if result . skip ] ) |
def close ( self ) :
"""Shutdown and free all resources .""" | if self . _controller is not None :
self . _controller . quit ( )
self . _controller = None
if self . _process is not None :
self . _process . close ( )
self . _process = None |
def cov_from_scales ( self , scales ) :
"""Return a covariance matrix built from a dictionary of scales .
` scales ` is a dictionary keyed by stochastic instances , and the
values refer are the variance of the jump distribution for each
stochastic . If a stochastic is a sequence , the variance must
have the... | # Get array of scales
ord_sc = [ ]
for stochastic in self . stochastics :
ord_sc . append ( np . ravel ( scales [ stochastic ] ) )
ord_sc = np . concatenate ( ord_sc )
if np . squeeze ( ord_sc ) . shape [ 0 ] != self . dim :
raise ValueError ( "Improper initial scales, dimension don't match" , ( np . squeeze ( ... |
def concentric_hexagons ( radius , start = ( 0 , 0 ) ) :
"""A generator which produces coordinates of concentric rings of hexagons .
Parameters
radius : int
Number of layers to produce ( 0 is just one hexagon )
start : ( x , y )
The coordinate of the central hexagon .""" | x , y = start
yield ( x , y )
for r in range ( 1 , radius + 1 ) : # Move to the next layer
y -= 1
# Walk around the hexagon of this radius
for dx , dy in [ ( 1 , 1 ) , ( 0 , 1 ) , ( - 1 , 0 ) , ( - 1 , - 1 ) , ( 0 , - 1 ) , ( 1 , 0 ) ] :
for _ in range ( r ) :
yield ( x , y )
... |
def _reaction_representer ( dumper , data ) :
"""Generate a parsable reaction representation to the YAML parser .
Check the number of compounds in the reaction , if it is larger than 10,
then transform the reaction data into a list of directories with all
attributes in the reaction ; otherwise , just return t... | if len ( data . compounds ) > _MAX_REACTION_LENGTH :
def dict_make ( compounds ) :
for compound , value in compounds :
yield OrderedDict ( [ ( 'id' , text_type ( compound . name ) ) , ( 'compartment' , compound . compartment ) , ( 'value' , value ) ] )
left = list ( dict_make ( data . left )... |
def get_message ( self , set_slave_ok , is_mongos , use_cmd = False ) :
"""Get a query message , possibly setting the slaveOk bit .""" | if set_slave_ok : # Set the slaveOk bit .
flags = self . flags | 4
else :
flags = self . flags
ns = _UJOIN % ( self . db , self . coll )
spec = self . spec
if use_cmd :
ns = _UJOIN % ( self . db , "$cmd" )
spec = self . as_command ( ) [ 0 ]
ntoreturn = - 1
# All DB commands return 1 document
els... |
def add_formdata ( self , content = None ) : # type : ( Optional [ Dict [ str , str ] ] ) - > None
"""Add data as a multipart form - data request to the request .
We only deal with file - like objects or strings at this point .
The requests is not yet streamed .
: param dict headers : Any headers to add to th... | if content is None :
content = { }
content_type = self . headers . pop ( 'Content-Type' , None ) if self . headers else None
if content_type and content_type . lower ( ) == 'application/x-www-form-urlencoded' : # Do NOT use " add _ content " that assumes input is JSON
self . data = { f : d for f , d in content ... |
def await_reservations ( self , sc , status = { } , timeout = 600 ) :
"""Block until all reservations are received .""" | timespent = 0
while not self . reservations . done ( ) :
logging . info ( "waiting for {0} reservations" . format ( self . reservations . remaining ( ) ) )
# check status flags for any errors
if 'error' in status :
sc . cancelAllJobs ( )
sc . stop ( )
sys . exit ( 1 )
time . slee... |
def headercontent ( self , method ) :
"""Get the content for the SOAP I { Header } node .
@ param method : A service method .
@ type method : I { service . Method }
@ return : The XML content for the < body / > .
@ rtype : [ L { Element } , . . . ]""" | content = [ ]
wsse = self . options ( ) . wsse
if wsse is not None :
content . append ( wsse . xml ( ) )
headers = self . options ( ) . soapheaders
if not isinstance ( headers , ( tuple , list , dict ) ) :
headers = ( headers , )
elif not headers :
return content
pts = self . headpart_types ( method )
if is... |
def set_chime ( self , sound , cycles = None ) :
""": param sound : a str , one of [ " doorbell " , " fur _ elise " , " doorbell _ extended " , " alert " ,
" william _ tell " , " rondo _ alla _ turca " , " police _ siren " ,
" " evacuation " , " beep _ beep " , " beep " , " inactive " ]
: param cycles : Undoc... | desired_state = { "activate_chime" : sound }
if cycles is not None :
desired_state . update ( { "chime_cycles" : cycles } )
response = self . api_interface . set_device_state ( self , { "desired_state" : desired_state } )
self . _update_state_from_response ( response ) |
def _set_factory_context ( factory_class , bundle_context ) : # type : ( type , Optional [ BundleContext ] ) - > Optional [ FactoryContext ]
"""Transforms the context data dictionary into its FactoryContext object form .
: param factory _ class : A manipulated class
: param bundle _ context : The class bundle c... | try : # Try to get the factory context ( built using decorators )
context = getattr ( factory_class , constants . IPOPO_FACTORY_CONTEXT )
except AttributeError : # The class has not been manipulated , or too badly
return None
if not context . completed : # Partial context ( class not manipulated )
return No... |
def execute_on_entries ( self , entry_processor , predicate = None ) :
"""Applies the user defined EntryProcessor to all the entries in the map or entries in the map which satisfies
the predicate if provided . Returns the results mapped by each key in the map .
: param entry _ processor : ( object ) , A statefu... | if predicate :
return self . _encode_invoke ( map_execute_with_predicate_codec , entry_processor = self . _to_data ( entry_processor ) , predicate = self . _to_data ( predicate ) )
return self . _encode_invoke ( map_execute_on_all_keys_codec , entry_processor = self . _to_data ( entry_processor ) ) |
def add_send_message ( self , connection , send_message ) :
"""Adds a send _ message function to the Dispatcher ' s
dictionary of functions indexed by connection .
Args :
connection ( str ) : A locally unique identifier
provided by the receiver of messages .
send _ message ( fn ) : The method that should ... | self . _send_message [ connection ] = send_message
LOGGER . debug ( "Added send_message function " "for connection %s" , connection ) |
def read_gaf ( fin_gaf , prt = sys . stdout , hdr_only = False , allow_missing_symbol = False , ** kws ) :
"""Read Gene Association File ( GAF ) . Return data .""" | return GafReader ( fin_gaf , hdr_only , prt = prt , allow_missing_symbol = allow_missing_symbol ) . get_id2gos ( ** kws ) |
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