signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def reciprocal_lattice_from_outcar ( filename ) : # from https : / / github . com / MaterialsDiscovery / PyChemia
"""Finds and returns the reciprocal lattice vectors , if more than
one set present , it just returns the last one .
Args :
filename ( Str ) : The name of the outcar file to be read
Returns :
L... | outcar = open ( filename , "r" ) . read ( )
# just keeping the last component
recLat = re . findall ( r"reciprocal\s*lattice\s*vectors\s*([-.\s\d]*)" , outcar ) [ - 1 ]
recLat = recLat . split ( )
recLat = np . array ( recLat , dtype = float )
# up to now I have , both direct and rec . lattices ( 3 + 3 = 6 columns )
re... |
def default_resolve_fn ( source , info , ** args ) : # type : ( Any , ResolveInfo , * * Any ) - > Optional [ Any ]
"""If a resolve function is not given , then a default resolve behavior is used which takes the property of the source object
of the same name as the field and returns it as the result , or if it ' s... | name = info . field_name
if isinstance ( source , dict ) :
property = source . get ( name )
else :
property = getattr ( source , name , None )
if callable ( property ) :
return property ( )
return property |
def _process_raw_report ( self , raw_report ) :
"Default raw input report data handler" | if not self . is_opened ( ) :
return
if not self . __evt_handlers and not self . __raw_handler :
return
if not raw_report [ 0 ] and ( raw_report [ 0 ] not in self . __input_report_templates ) : # windows sends an empty array when disconnecting
# but , this might have a collision with report _ id = 0
if not ... |
def stop ( self ) :
"""Stop consuming the stream and shutdown the background thread .""" | with self . _operational_lock :
self . _bidi_rpc . close ( )
if self . _thread is not None : # Resume the thread to wake it up in case it is sleeping .
self . resume ( )
self . _thread . join ( )
self . _thread = None |
def abort ( payment ) :
"""Abort a payment from its id .
: param payment : The payment id or payment object
: type payment : string | Payment
: return : The payment resource
: rtype : resources . Payment""" | if isinstance ( payment , resources . Payment ) :
payment = payment . id
http_client = HttpClient ( )
response , __ = http_client . patch ( routes . url ( routes . PAYMENT_RESOURCE , resource_id = payment ) , { 'abort' : True } )
return resources . Payment ( ** response ) |
def _split_coefficents ( self , w ) :
"""Split into intercept / bias and feature - specific coefficients""" | if self . _fit_intercept :
bias = w [ 0 ]
wf = w [ 1 : ]
else :
bias = 0.0
wf = w
return bias , wf |
def reset ( self ) :
"""Instruct the target to forget any related exception .""" | if not self . chain_id :
return
saved , self . chain_id = self . chain_id , None
try :
self . call_no_reply ( mitogen . core . Dispatcher . forget_chain , saved )
finally :
self . chain_id = saved |
def add_particles_ascii ( self , s ) :
"""Adds particles from an ASCII string .
Parameters
s : string
One particle per line . Each line should include particle ' s mass , radius , position and velocity .""" | for l in s . split ( "\n" ) :
r = l . split ( )
if len ( r ) :
try :
r = [ float ( x ) for x in r ]
p = Particle ( simulation = self , m = r [ 0 ] , r = r [ 1 ] , x = r [ 2 ] , y = r [ 3 ] , z = r [ 4 ] , vx = r [ 5 ] , vy = r [ 6 ] , vz = r [ 7 ] )
self . add ( p )
... |
def siblings ( self , ** kwargs ) :
"""Retrieve the other activities that also belong to the parent .
It returns a combination of Tasks ( a . o . UserTasks ) and Subprocesses on the level of the current task , including
itself . This also works if the activity is of type ` ActivityType . PROCESS ` .
: param k... | parent_id = self . _json_data . get ( 'parent_id' )
if parent_id is None :
raise NotFoundError ( "Cannot find subprocess for this task '{}', " "as this task exist on top level." . format ( self . name ) )
return self . _client . activities ( parent_id = parent_id , scope = self . scope_id , ** kwargs ) |
def send ( self , request , ** kwargs ) : # type : ( ClientRequest , Any ) - > ClientResponse
"""Send request object according to configuration .
Allowed kwargs are :
- session : will override the driver session and use yours . Should NOT be done unless really required .
- anything else is sent straight to re... | # It ' s not recommended to provide its own session , and is mostly
# to enable some legacy code to plug correctly
session = kwargs . pop ( 'session' , self . session )
try :
response = session . request ( request . method , request . url , ** kwargs )
except requests . RequestException as err :
msg = "Error oc... |
def _extract_upnperror ( self , err_xml ) :
"""Extract the error code and error description from an error returned by the device .""" | nsmap = { 's' : list ( err_xml . nsmap . values ( ) ) [ 0 ] }
fault_str = err_xml . findtext ( 's:Body/s:Fault/faultstring' , namespaces = nsmap )
try :
err = err_xml . xpath ( 's:Body/s:Fault/detail/*[name()="%s"]' % fault_str , namespaces = nsmap ) [ 0 ]
except IndexError :
msg = 'Tag with name of %r was not ... |
def list_overlay_names ( self ) :
"""Return list of overlay names .""" | overlay_names = [ ]
if not os . path . isdir ( self . _overlays_abspath ) :
return overlay_names
for fname in os . listdir ( self . _overlays_abspath ) :
name , ext = os . path . splitext ( fname )
overlay_names . append ( name )
return overlay_names |
def alignProcrustes ( sources , rigid = False ) :
"""Return an ` ` Assembly ` ` of aligned source actors with
the ` Procrustes ` algorithm . The output ` ` Assembly ` ` is normalized in size .
` Procrustes ` algorithm takes N set of points and aligns them in a least - squares sense
to their mutual mean . The ... | group = vtk . vtkMultiBlockDataGroupFilter ( )
for source in sources :
if sources [ 0 ] . N ( ) != source . N ( ) :
vc . printc ( "~times Procrustes error in align():" , c = 1 )
vc . printc ( " sources have different nr of points" , c = 1 )
exit ( 0 )
group . AddInputData ( source . poly... |
def diy ( expression_data , regressor_type , regressor_kwargs , gene_names = None , tf_names = 'all' , client_or_address = 'local' , early_stop_window_length = EARLY_STOP_WINDOW_LENGTH , limit = None , seed = None , verbose = False ) :
""": param expression _ data : one of :
* a pandas DataFrame ( rows = observat... | if verbose :
print ( 'preparing dask client' )
client , shutdown_callback = _prepare_client ( client_or_address )
try :
if verbose :
print ( 'parsing input' )
expression_matrix , gene_names , tf_names = _prepare_input ( expression_data , gene_names , tf_names )
if verbose :
print ( 'crea... |
def impute ( args ) :
"""% prog impute input . vcf hs37d5 . fa 1
Use IMPUTE2 to impute vcf on chromosome 1.""" | from pyfaidx import Fasta
p = OptionParser ( impute . __doc__ )
p . set_home ( "shapeit" )
p . set_home ( "impute" )
p . set_ref ( )
p . set_cpus ( )
opts , args = p . parse_args ( args )
if len ( args ) != 3 :
sys . exit ( not p . print_help ( ) )
vcffile , fastafile , chr = args
mm = MakeManager ( )
pf = vcffile ... |
def unpin_chat_message ( self , chat_id : Union [ int , str ] ) -> bool :
"""Use this method to unpin a message in a group , channel or your own chat .
You must be an administrator in the chat for this to work and must have the " can _ pin _ messages " admin
right in the supergroup or " can _ edit _ messages " ... | self . send ( functions . messages . UpdatePinnedMessage ( peer = self . resolve_peer ( chat_id ) , id = 0 ) )
return True |
def get_entry_map ( self , group = None ) :
"""Return the entry point map for ` group ` , or the full entry map""" | try :
ep_map = self . _ep_map
except AttributeError :
ep_map = self . _ep_map = EntryPoint . parse_map ( self . _get_metadata ( 'entry_points.txt' ) , self )
if group is not None :
return ep_map . get ( group , { } )
return ep_map |
def _plot_weights_motif ( self , index , plot_type = "motif_raw" , background_probs = DEFAULT_BASE_BACKGROUND , ncol = 1 , figsize = None ) :
"""Index can only be a single int""" | w_all = self . get_weights ( )
if len ( w_all ) == 0 :
raise Exception ( "Layer needs to be initialized first" )
W = w_all [ 0 ]
if index is None :
index = np . arange ( W . shape [ 2 ] )
if isinstance ( index , int ) :
index = [ index ]
fig = plt . figure ( figsize = figsize )
if plot_type == "motif_pwm" a... |
def choices ( self ) :
"""Available choices for characters to be generated .""" | if self . _choices :
return self . _choices
for n in os . listdir ( self . _voicedir ) :
if len ( n ) == 1 and os . path . isdir ( os . path . join ( self . _voicedir , n ) ) :
self . _choices . append ( n )
return self . _choices |
def getContactTypes ( self ) :
"""Return an iterator of L { IContactType } providers available to this
organizer ' s store .""" | yield VIPPersonContactType ( )
yield EmailContactType ( self . store )
yield PostalContactType ( )
yield PhoneNumberContactType ( )
yield NotesContactType ( )
for getContactTypes in self . _gatherPluginMethods ( 'getContactTypes' ) :
for contactType in getContactTypes ( ) :
self . _checkContactType ( contac... |
def money_flow_index ( close_data , high_data , low_data , volume , period ) :
"""Money Flow Index .
Formula :
MFI = 100 - ( 100 / ( 1 + PMF / NMF ) )""" | catch_errors . check_for_input_len_diff ( close_data , high_data , low_data , volume )
catch_errors . check_for_period_error ( close_data , period )
mf = money_flow ( close_data , high_data , low_data , volume )
tp = typical_price ( close_data , high_data , low_data )
flow = [ tp [ idx ] > tp [ idx - 1 ] for idx in ran... |
def extracted ( name , source , source_hash = None , source_hash_name = None , source_hash_update = False , skip_verify = False , password = None , options = None , list_options = None , force = False , overwrite = False , clean = False , user = None , group = None , if_missing = None , trim_output = False , use_cmd_un... | ret = { 'name' : name , 'result' : False , 'changes' : { } , 'comment' : '' }
# Remove pub kwargs as they ' re irrelevant here .
kwargs = salt . utils . args . clean_kwargs ( ** kwargs )
if 'keep_source' in kwargs and 'keep' in kwargs :
ret . setdefault ( 'warnings' , [ ] ) . append ( 'Both \'keep_source\' and \'ke... |
def changes ( self , adding = None , deleting = None ) :
"""Pass the given changes to the root _ node .""" | if deleting is not None :
for deleted in deleting :
self . root_node . remove ( deleted )
if adding is not None :
for added in adding :
self . root_node . add ( added )
added = list ( )
removed = list ( )
for csn in self . _get_conflict_set_nodes ( ) :
c_added , c_removed = csn . get_activat... |
def nla_for_each_attr ( head , len_ , rem ) :
"""Iterate over a stream of attributes .
https : / / github . com / thom311 / libnl / blob / libnl3_2_25 / include / netlink / attr . h # L262
Positional arguments :
head - - first nlattr with more in its bytearray payload ( nlattr class instance ) .
len _ - - l... | pos = head
rem . value = len_
while nla_ok ( pos , rem ) :
yield pos
pos = nla_next ( pos , rem ) |
def docelement ( self ) :
"""Returns the instance of the element whose body owns the docstring
in the current operation .""" | # This is needed since the decorating documentation
# for types and executables is in the body of the module , but when they
# get edited , the edit belongs to the type / executable because the character
# falls within the absstart and end attributes .
if self . _docelement is None :
if isinstance ( self . element ... |
def add_case ( self , case , update = False ) :
"""Add a case to the case collection
If the case exists and update is False raise error .
Args :
db ( MongoClient ) : A connection to the mongodb
case ( dict ) : A case dictionary
update ( bool ) : If existing case should be updated
Returns :
mongo _ cas... | existing_case = self . case ( case )
if existing_case and not update :
raise CaseError ( "Case {} already exists" . format ( case [ 'case_id' ] ) )
if existing_case :
self . db . case . find_one_and_replace ( { 'case_id' : case [ 'case_id' ] } , case , )
else :
self . db . case . insert_one ( case )
return ... |
def freeze_bn ( self ) :
'''Freeze BatchNorm layers .''' | for layer in self . modules ( ) :
if isinstance ( layer , nn . BatchNorm2d ) :
layer . eval ( ) |
def update ( cls , cluster_id_label , cluster_info ) :
"""Update the cluster with id / label ` cluster _ id _ label ` using information provided in
` cluster _ info ` .""" | conn = Qubole . agent ( version = "v2" )
return conn . put ( cls . element_path ( cluster_id_label ) , data = cluster_info ) |
def termination_check ( self ) : # type : ( Uploader ) - > bool
"""Check if terminated
: param Uploader self : this
: rtype : bool
: return : if terminated""" | with self . _upload_lock :
with self . _transfer_lock :
return ( self . _upload_terminate or len ( self . _exceptions ) > 0 or ( self . _all_files_processed and len ( self . _upload_set ) == 0 and len ( self . _transfer_set ) == 0 ) ) |
def load_vocab ( vocab_file ) :
"""Loads a vocabulary file into a dictionary .""" | vocab = collections . OrderedDict ( )
index = 0
with io . open ( vocab_file , 'r' ) as reader :
while True :
token = reader . readline ( )
if not token :
break
token = token . strip ( )
vocab [ token ] = index
index += 1
return vocab |
def to_twos_comp ( val , bits ) :
"""compute the 2 ' s compliment of int value val""" | if not val . startswith ( '-' ) :
return to_int ( val )
value = _invert ( to_bin_str_from_int_string ( bits , bin ( to_int ( val [ 1 : ] ) ) ) )
return int ( value , 2 ) + 1 |
def convert_upload_string_to_file ( i ) :
"""Input : {
file _ content _ base64 - string transmitted through Internet
( filename ) - file name to write ( if empty , generate tmp file )
Output : {
return - return code = 0 , if successful
> 0 , if error
( error ) - error text if return > 0
filename - fil... | import base64
x = i [ 'file_content_base64' ]
fc = base64 . urlsafe_b64decode ( str ( x ) )
# convert from unicode to str since base64 works on strings
# should be safe in Python 2 . x and 3 . x
fn = i . get ( 'filename' , '' )
if fn == '' :
rx = gen_tmp_file ( { 'prefix' : 'tmp-' } )
if rx [ 'return' ] > 0 :
... |
def relation_column ( instance , fields ) :
'''such as : user . username
such as : replies . content''' | relation = getattr ( instance . __class__ , fields [ 0 ] ) . property
_field = getattr ( instance , fields [ 0 ] )
if relation . lazy == 'dynamic' :
_field = _field . first ( )
return getattr ( _field , fields [ 1 ] ) if _field else '' |
def get_image_path ( name , default = "not_found.png" ) :
"""Return image absolute path""" | for img_path in IMG_PATH :
full_path = osp . join ( img_path , name )
if osp . isfile ( full_path ) :
return osp . abspath ( full_path )
if default is not None :
img_path = osp . join ( get_module_path ( 'spyder' ) , 'images' )
return osp . abspath ( osp . join ( img_path , default ) ) |
def handle ( self , * args , ** options ) :
"""Main command method .""" | # Already running , so quit
if os . path . exists ( self . lock_file ) :
self . log ( ( "This script is already running. " "(If your are sure it's not please " "delete the lock file in {}')" ) . format ( self . lock_file ) )
sys . exit ( 0 )
if not os . path . exists ( os . path . dirname ( self . lock_file ) )... |
def dataSource ( self , value ) :
"""sets the datasource object""" | if isinstance ( value , DataSource ) :
self . _dataSource = value
else :
raise TypeError ( "value must be a DataSource object" ) |
def start ( self ) :
"""Begin listening for events from the Client and acting upon them .
Note : If configuration has not already been loaded , it will be loaded
immediately before starting to listen for events . Calling this method
without having specified and / or loaded a configuration will result in
com... | if not self . config and self . config_path is not None :
self . load_config ( )
self . running = True
self . process_event ( "STARTUP" , self . client , ( ) ) |
def _invade_isolated_Ts ( self ) :
r"""Throats that are uninvaded connected to pores that are both invaded
should be invaded too .""" | net = self . project . network
Ts = net [ 'throat.conns' ] . copy ( )
invaded_Ps = self [ 'pore.invasion_sequence' ] > - 1
uninvaded_Ts = self [ 'throat.invasion_sequence' ] == - 1
isolated_Ts = np . logical_and ( invaded_Ps [ Ts [ : , 0 ] ] , invaded_Ps [ Ts [ : , 1 ] ] )
isolated_Ts = np . logical_and ( isolated_Ts ,... |
def convert_multiple_sources_to_consumable_types ( self , project , prop_set , sources ) :
"""Converts several files to consumable types .""" | if __debug__ :
from . targets import ProjectTarget
assert isinstance ( project , ProjectTarget )
assert isinstance ( prop_set , property_set . PropertySet )
assert is_iterable_typed ( sources , virtual_target . VirtualTarget )
if not self . source_types_ :
return list ( sources )
acceptable_types = ... |
def check_for_update ( self , force = True , download = False ) :
"""Returns a : class : ` ~ plexapi . base . Release ` object containing release info .
Parameters :
force ( bool ) : Force server to check for new releases
download ( bool ) : Download if a update is available .""" | part = '/updater/check?download=%s' % ( 1 if download else 0 )
if force :
self . query ( part , method = self . _session . put )
releases = self . fetchItems ( '/updater/status' )
if len ( releases ) :
return releases [ 0 ] |
def save_anndata ( self , fname , data = 'adata_raw' , ** kwargs ) :
"""Saves ` adata _ raw ` to a . h5ad file ( AnnData ' s native file format ) .
Parameters
fname - string
The filename of the output file .""" | x = self . __dict__ [ data ]
x . write_h5ad ( fname , ** kwargs ) |
def notify_scale_factor_change ( self , screen_id , u32_scale_factor_w_multiplied , u32_scale_factor_h_multiplied ) :
"""Notify OpenGL HGCM host service about graphics content scaling factor change .
in screen _ id of type int
in u32 _ scale _ factor _ w _ multiplied of type int
in u32 _ scale _ factor _ h _ ... | if not isinstance ( screen_id , baseinteger ) :
raise TypeError ( "screen_id can only be an instance of type baseinteger" )
if not isinstance ( u32_scale_factor_w_multiplied , baseinteger ) :
raise TypeError ( "u32_scale_factor_w_multiplied can only be an instance of type baseinteger" )
if not isinstance ( u32_... |
def check_retcode ( self , line ) :
"""Look for retcode on line line and return return code if found .
: param line : Line to search from
: return : integer return code or - 1 if " cmd tasklet init " is found . None if retcode or cmd
tasklet init not found .""" | retcode = None
match = re . search ( r"retcode\: ([-\d]{1,})" , line )
if match :
retcode = num ( str ( match . group ( 1 ) ) )
match = re . search ( "cmd tasklet init" , line )
if match :
self . logger . debug ( "Device Boot up" , extra = { 'type' : ' ' } )
return - 1
return retcode |
def display ( self , ret , indent , out , rows_key = None , labels_key = None ) :
'''Display table ( s ) .''' | rows = [ ]
labels = None
if isinstance ( ret , dict ) :
if not rows_key or ( rows_key and rows_key in list ( ret . keys ( ) ) ) : # either not looking for a specific key
# either looking and found in the current root
for key in sorted ( ret ) :
if rows_key and key != rows_key :
... |
def start ( self , name ) :
'''End the current behaviour and run a named behaviour .
: param name : the name of the behaviour to run
: type name : str''' | d = self . boatd . post ( { 'active' : name } , endpoint = '/behaviours' )
current = d . get ( 'active' )
if current is not None :
return 'started {}' . format ( current )
else :
return 'no behaviour running' |
def min_date ( self , symbol ) :
"""Return the minimum datetime stored for a particular symbol
Parameters
symbol : ` str `
symbol name for the item""" | res = self . _collection . find_one ( { SYMBOL : symbol } , projection = { ID : 0 , START : 1 } , sort = [ ( START , pymongo . ASCENDING ) ] )
if res is None :
raise NoDataFoundException ( "No Data found for {}" . format ( symbol ) )
return utc_dt_to_local_dt ( res [ START ] ) |
def select_template ( template_name_list , using = None ) :
"""Loads and returns a template for one of the given names .
Tries names in order and returns the first template found .
Raises TemplateDoesNotExist if no such template exists .""" | if isinstance ( template_name_list , six . string_types ) :
raise TypeError ( 'select_template() takes an iterable of template names but got a ' 'string: %r. Use get_template() if you want to load a single ' 'template by name.' % template_name_list )
engines = _engine_list ( using )
for template_name in template_na... |
def get_comic_format ( filename ) :
"""Return the comic format if it is a comic archive .""" | image_format = None
filename_ext = os . path . splitext ( filename ) [ - 1 ] . lower ( )
if filename_ext in _COMIC_EXTS :
if zipfile . is_zipfile ( filename ) :
image_format = _CBZ_FORMAT
elif rarfile . is_rarfile ( filename ) :
image_format = _CBR_FORMAT
return image_format |
def get_lattice_vector_equivalence ( point_symmetry ) :
"""Return ( b = = c , c = = a , a = = b )""" | # primitive _ vectors : column vectors
equivalence = [ False , False , False ]
for r in point_symmetry :
if ( np . abs ( r [ : , 0 ] ) == [ 0 , 1 , 0 ] ) . all ( ) :
equivalence [ 2 ] = True
if ( np . abs ( r [ : , 0 ] ) == [ 0 , 0 , 1 ] ) . all ( ) :
equivalence [ 1 ] = True
if ( np . abs (... |
def info ( self , msg : str ) -> None :
"""Write an info message to the Windows Application log
( ± to the Python disk log ) .""" | # noinspection PyUnresolvedReferences
s = "{}: {}" . format ( self . fullname , msg )
servicemanager . LogInfoMsg ( s )
if self . debugging :
log . info ( s ) |
def predict_is ( self , h = 5 , fit_once = True ) :
"""Makes dynamic in - sample predictions with the estimated model
Parameters
h : int ( default : 5)
How many steps would you like to forecast ?
fit _ once : boolean
( default : True ) Fits only once before the in - sample prediction ; if False , fits aft... | predictions = [ ]
for t in range ( 0 , h ) :
x = NLLEV ( family = self . family , integ = self . integ , data = self . data_original [ : ( - h + t ) ] )
x . fit ( print_progress = False )
if t == 0 :
predictions = x . predict ( h = 1 )
else :
predictions = pd . concat ( [ predictions , x... |
def _log ( self , num = None , format = None ) :
'''Helper function to receive git log
: param num :
Number of entries
: param format :
Use formatted output with specified format string''' | num = '-n %s' % ( num ) if num else ''
format = '--format="%s"' % ( format ) if format else ''
return self . m ( 'getting git log' , cmdd = dict ( cmd = 'git log %s %s' % ( num , format ) , cwd = self . local ) , verbose = False ) |
def _UpdateSudoer ( self , user , sudoer = False ) :
"""Update sudoer group membership for a Linux user account .
Args :
user : string , the name of the Linux user account .
sudoer : bool , True if the user should be a sudoer .
Returns :
bool , True if user update succeeded .""" | if sudoer :
self . logger . info ( 'Adding user %s to the Google sudoers group.' , user )
command = self . gpasswd_add_cmd . format ( user = user , group = self . google_sudoers_group )
else :
self . logger . info ( 'Removing user %s from the Google sudoers group.' , user )
command = self . gpasswd_remo... |
def MaximumLikelihood ( self ) :
"""Returns the value with the highest probability .
Returns : float probability""" | prob , val = max ( ( prob , val ) for val , prob in self . Items ( ) )
return val |
def _handler ( self , conn ) :
"""Connection handler thread . Takes care of communication with the client
and running the proper task or applying a signal .""" | incoming = self . recv ( conn )
self . log ( DEBUG , incoming )
try : # E . g . [ ' twister ' , [ 7 , ' invert ' ] , { ' guess _ type ' : True } ]
task , args , kw = self . codec . decode ( incoming )
# OK , so we ' ve received the information . Now to use it .
self . log ( INFO , 'Fulfilling task %r' % tas... |
def lookup_ids ( self , keys ) :
"""Lookup the integer ID associated with each ( namespace , key ) in the
keys list""" | keys_len = len ( keys )
ids = { namespace_key : None for namespace_key in keys }
start = 0
bulk_insert = self . bulk_insert
query = 'SELECT namespace, key, id FROM gauged_keys WHERE '
check = '(namespace = %s AND key = %s) '
cursor = self . cursor
execute = cursor . execute
while start < keys_len :
rows = keys [ st... |
def ecliptic_xyz ( self , epoch = None ) :
"""Compute J2000 ecliptic position vector ( x , y , z ) .
If you instead want the coordinates referenced to the dynamical
system defined by the Earth ' s true equator and equinox , provide
an epoch time .""" | if epoch is None :
vector = _ECLIPJ2000 . dot ( self . position . au )
return Distance ( vector )
position_au = self . position . au
if isinstance ( epoch , Time ) :
pass
elif isinstance ( epoch , float ) :
epoch = Time ( None , tt = epoch )
elif epoch == 'date' :
epoch = self . t
else :
raise V... |
def libvlc_event_attach ( p_event_manager , i_event_type , f_callback , user_data ) :
'''Register for an event notification .
@ param p _ event _ manager : the event manager to which you want to attach to . Generally it is obtained by vlc _ my _ object _ event _ manager ( ) where my _ object is the object you wan... | f = _Cfunctions . get ( 'libvlc_event_attach' , None ) or _Cfunction ( 'libvlc_event_attach' , ( ( 1 , ) , ( 1 , ) , ( 1 , ) , ( 1 , ) , ) , None , ctypes . c_int , EventManager , ctypes . c_uint , Callback , ctypes . c_void_p )
return f ( p_event_manager , i_event_type , f_callback , user_data ) |
def startAlertListener ( self , callback = None ) :
"""Creates a websocket connection to the Plex Server to optionally recieve
notifications . These often include messages from Plex about media scans
as well as updates to currently running Transcode Sessions .
NOTE : You need websocket - client installed in o... | notifier = AlertListener ( self , callback )
notifier . start ( )
return notifier |
def obfuscatable_variable ( tokens , index , ignore_length = False ) :
"""Given a list of * tokens * and an * index * ( representing the current position ) ,
returns the token string if it is a variable name that can be safely
obfuscated .
Returns ' _ _ skipline _ _ ' if the rest of the tokens on this line sh... | tok = tokens [ index ]
token_type = tok [ 0 ]
token_string = tok [ 1 ]
line = tok [ 4 ]
if index > 0 :
prev_tok = tokens [ index - 1 ]
else : # Pretend it ' s a newline ( for simplicity )
prev_tok = ( 54 , '\n' , ( 1 , 1 ) , ( 1 , 2 ) , '#\n' )
prev_tok_type = prev_tok [ 0 ]
prev_tok_string = prev_tok [ 1 ]
try... |
def fixchars ( self , text ) :
"""Find and replace problematic characters .""" | keys = '' . join ( Config . CHARFIXES . keys ( ) )
values = '' . join ( Config . CHARFIXES . values ( ) )
fixed = text . translate ( str . maketrans ( keys , values ) )
if fixed != text :
self . modified = True
return fixed |
def get_interface_detail_output_interface_ifHCInOctets ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
get_interface_detail = ET . Element ( "get_interface_detail" )
config = get_interface_detail
output = ET . SubElement ( get_interface_detail , "output" )
interface = ET . SubElement ( output , "interface" )
interface_type_key = ET . SubElement ( interface , "interface-type" )
interfac... |
def report_parse ( self ) :
"""If the pipeline has previously been run on these data , instead of reading through the results , parse the
report instead""" | # Initialise lists
report_strains = list ( )
genus_list = list ( )
if self . analysistype == 'mlst' :
for sample in self . runmetadata . samples :
try :
genus_list . append ( sample . general . referencegenus )
except AttributeError :
sample . general . referencegenus = 'ND'
... |
def get_errors ( audit_results ) :
"""Args :
audit _ results : results of ` AxsAudit . do _ audit ( ) ` .
Returns : a list of errors .""" | errors = [ ]
if audit_results :
if audit_results . errors :
errors . extend ( audit_results . errors )
return errors |
def sort_dictionary_list ( dict_list , sort_key ) :
"""sorts a list of dictionaries based on the value of the sort _ key
dict _ list - a list of dictionaries
sort _ key - a string that identifies the key to sort the dictionaries with .
Test sorting a list of dictionaries :
> > > sort _ dictionary _ list ( [... | if not dict_list or len ( dict_list ) == 0 :
return dict_list
dict_list . sort ( key = itemgetter ( sort_key ) )
return dict_list |
def name ( self , value ) :
"""Generate the Site ' s slug ( for file paths , URL ' s , etc . )""" | self . _name = value
self . slug = re . sub ( '[^0-9a-zA-Z_-]+' , '_' , str ( value ) . lower ( ) )
self . root = os . path . abspath ( os . path . join ( _cfg . get ( 'Paths' , 'HttpRoot' ) , self . domain . name , self . slug ) ) |
def get ( self , id ) :
"""Return the : class : ` ~ plexapi . settings . Setting ` object with the specified id .""" | id = utils . lowerFirst ( id )
if id in self . _settings :
return self . _settings [ id ]
raise NotFound ( 'Invalid setting id: %s' % id ) |
def replace_contractions_with_full_words_and_replace_numbers_with_digits ( text = None , remove_articles = True ) :
"""This function replaces contractions with full words and replaces numbers
with digits in specified text . There is the option to remove articles .""" | words = text . split ( )
text_translated = ""
for word in words :
if remove_articles and word in [ "a" , "an" , "the" ] :
continue
contractions_expansions = { "ain't" : "is not" , "aren't" : "are not" , "can't" : "can not" , "could've" : "could have" , "couldn't" : "could not" , "didn't" : "did not" , "... |
def _send_command_list ( self , commands ) :
"""Wrapper for Netmiko ' s send _ command method ( for list of commands .""" | output = ""
for command in commands :
output += self . device . send_command ( command , strip_prompt = False , strip_command = False )
return output |
def move_mouse_relative ( self , x , y ) :
"""Move the mouse relative to it ' s current position .
: param x : the distance in pixels to move on the X axis .
: param y : the distance in pixels to move on the Y axis .""" | _libxdo . xdo_move_mouse_relative ( self . _xdo , x , y ) |
def _kbhit_unix ( ) -> bool :
"""Under UNIX : is a keystroke available ?""" | dr , dw , de = select . select ( [ sys . stdin ] , [ ] , [ ] , 0 )
return dr != [ ] |
def plotFCM ( data , channel_names , kind = 'histogram' , ax = None , autolabel = True , xlabel_kwargs = { } , ylabel_kwargs = { } , colorbar = False , grid = False , ** kwargs ) :
"""Plots the sample on the current axis .
Follow with a call to matplotlibs show ( ) in order to see the plot .
Parameters
data :... | if ax == None :
ax = pl . gca ( )
xlabel_kwargs . setdefault ( 'size' , 16 )
ylabel_kwargs . setdefault ( 'size' , 16 )
channel_names = to_list ( channel_names )
if len ( channel_names ) == 1 : # 1D so histogram plot
kwargs . setdefault ( 'color' , 'gray' )
kwargs . setdefault ( 'histtype' , 'stepfilled' )
... |
def find_models ( self , constructor , constraints = None , * , columns = None , order_by = None , limiting = None , table_name = None ) :
"""Specialization of DataAccess . find _ all that returns models instead of cursor objects .""" | return self . _find_models ( constructor , table_name or constructor . table_name , constraints , columns = columns , order_by = order_by , limiting = limiting ) |
def inner_rect ( self ) :
"""The rectangular area inside the margin , border , and padding .
Generally widgets should avoid drawing or placing sub - widgets outside
this rectangle .""" | m = self . margin + self . _border_width + self . padding
if not self . border_color . is_blank :
m += 1
return Rect ( ( m , m ) , ( self . size [ 0 ] - 2 * m , self . size [ 1 ] - 2 * m ) ) |
def _UpdateAndMigrateUnmerged ( self , not_merged_stops , zone_map , merge_map , schedule ) :
"""Correct references in migrated unmerged stops and add to merged _ schedule .
For stops migrated from one of the input feeds to the output feed update the
parent _ station and zone _ id references to point to objects... | # for the unmerged stops , we use an already mapped zone _ id if possible
# if not , we generate a new one and add it to the map
for stop , migrated_stop in not_merged_stops :
if stop . zone_id in zone_map :
migrated_stop . zone_id = zone_map [ stop . zone_id ]
else :
migrated_stop . zone_id = s... |
def fetch_digests ( self , package_name : str , package_version : str ) -> dict :
"""Fetch digests for the given package in specified version from the given package index .""" | report = { }
for source in self . _sources :
try :
report [ source . url ] = source . get_package_hashes ( package_name , package_version )
except NotFound as exc :
_LOGGER . debug ( f"Package {package_name} in version {package_version} not " f"found on index {source.name}: {str(exc)}" )
return ... |
def set ( self , oid , value , value_type = None ) :
"""Sets a single OID value . If you do not pass value _ type hnmp will
try to guess the correct type . Autodetection is supported for :
* int and float ( as Integer , fractional part will be discarded )
* IPv4 address ( as IpAddress )
* str ( as OctetStri... | snmpsecurity = self . _get_snmp_security ( )
if value_type is None :
if isinstance ( value , int ) :
data = Integer ( value )
elif isinstance ( value , float ) :
data = Integer ( value )
elif isinstance ( value , str ) :
if is_ipv4_address ( value ) :
data = IpAddress ( v... |
def get_objective_search_session ( self ) :
"""Gets the OsidSession associated with the objective search
service .
return : ( osid . learning . ObjectiveSearchSession ) - an
ObjectiveSearchSession
raise : OperationFailed - unable to complete request
raise : Unimplemented - supports _ objective _ search ( ... | if not self . supports_objective_search ( ) :
raise Unimplemented ( )
try :
from . import sessions
except ImportError :
raise OperationFailed ( )
try :
session = sessions . ObjectiveSearchSession ( runtime = self . _runtime )
except AttributeError :
raise OperationFailed ( )
return session |
def parse_range_header ( header , maxlen = 0 ) :
'''Yield ( start , end ) ranges parsed from a HTTP Range header . Skip
unsatisfiable ranges . The end index is non - inclusive .''' | if not header or header [ : 6 ] != 'bytes=' :
return
ranges = [ r . split ( '-' , 1 ) for r in header [ 6 : ] . split ( ',' ) if '-' in r ]
for start , end in ranges :
try :
if not start : # bytes = - 100 - > last 100 bytes
start , end = max ( 0 , maxlen - int ( end ) ) , maxlen
elif... |
def compute_asset_lifetimes ( frames ) :
"""Parameters
frames : dict [ str , pd . DataFrame ]
A dict mapping each OHLCV field to a dataframe with a row for
each date and a column for each sid , as passed to write ( ) .
Returns
start _ date _ ixs : np . array [ int64]
The index of the first date with non... | # Build a 2D array ( dates x sids ) , where an entry is True if all
# fields are nan for the given day and sid .
is_null_matrix = np . logical_and . reduce ( [ frames [ field ] . isnull ( ) . values for field in FIELDS ] , )
if not is_null_matrix . size :
empty = np . array ( [ ] , dtype = 'int64' )
return empt... |
def fetch_object ( self , doc_id ) :
"""Fetch the document by its PK .""" | try :
return self . object_class . objects . get ( pk = doc_id )
except self . object_class . DoesNotExist :
raise ReferenceNotFoundError |
def reboot ( self ) :
"""Reboots the device .
Generally one should use this method to reboot the device instead of
directly calling ` adb . reboot ` . Because this method gracefully handles
the teardown and restoration of running services .
This method is blocking and only returns when the reboot has comple... | if self . is_bootloader :
self . fastboot . reboot ( )
return
with self . handle_reboot ( ) :
self . adb . reboot ( ) |
def verify ( self , ** kwargs ) :
"""Checks this component for invalidating conditions
: returns : str - - message if error , 0 otherwise""" | if 'duration' in kwargs :
if kwargs [ 'duration' ] < self . _duration :
return "Window size must equal or exceed stimulus length"
if self . _risefall > self . _duration :
return "Rise and fall times exceed component duration"
return 0 |
def encode_certificate ( result ) :
"""Encode cert bytes to PEM encoded cert file .""" | cert_body = """-----BEGIN CERTIFICATE-----\n{0}\n-----END CERTIFICATE-----\n""" . format ( "\n" . join ( textwrap . wrap ( base64 . b64encode ( result ) . decode ( 'utf8' ) , 64 ) ) )
signed_crt = open ( "{}/signed.crt" . format ( gettempdir ( ) ) , "w" )
signed_crt . write ( cert_body )
signed_crt . close ( )
return T... |
def show ( self ) :
"""Ensure the widget is shown .
Calling this method will also set the widget visibility to True .""" | self . visible = True
if self . proxy_is_active :
self . proxy . ensure_visible ( ) |
def mask ( scope , ips , mask ) :
"""Applies the given IP mask ( e . g . 255.255.255.0 ) to the given IP address
( or list of IP addresses ) and returns it .
: type ips : string
: param ips : A prefix , or a list of IP prefixes .
: type mask : string
: param mask : An IP mask .
: rtype : string
: retu... | mask = ipv4 . ip2int ( mask [ 0 ] )
return [ ipv4 . int2ip ( ipv4 . ip2int ( ip ) & mask ) for ip in ips ] |
def contains ( self , token : str ) -> bool :
"""Return if the token is in the list or not .""" | self . _validate_token ( token )
return token in self |
def delete_all_metadata ( self ) :
"""DELETE / : login / machines / : id / metadata
: Returns : current metadata
: rtype : empty : py : class : ` dict `
Deletes all the metadata stored for this machine . Also explicitly
requests and returns the machine metadata so that the local copy stays
synchronized ."... | j , r = self . datacenter . request ( 'DELETE' , self . path + '/metadata' )
r . raise_for_status ( )
return self . get_metadata ( ) |
def _write_proxy_conf ( proxyfile ) :
'''write to file''' | msg = 'Invalid value for proxy file provided!, Supplied value = {0}' . format ( proxyfile )
log . trace ( 'Salt Proxy Module: write proxy conf' )
if proxyfile :
log . debug ( 'Writing proxy conf file' )
with salt . utils . files . fopen ( proxyfile , 'w' ) as proxy_conf :
proxy_conf . write ( salt . uti... |
def get_locations ( self , filter_to_my_group = False ) :
"""Retrieve Locations listed in ChemInventory""" | resp = self . _post ( 'general-retrievelocations' , 'locations' )
groups = { }
if resp [ 'groupinfo' ] :
for group in resp [ 'groupinfo' ] :
groups [ group [ 'id' ] ] = Group ( name = group . get ( 'name' ) , inventory_id = group . get ( 'id' ) )
final_resp = [ ]
if resp [ 'data' ] :
if filter_to_my_gro... |
def solution_path ( self , min_lambda , max_lambda , lambda_bins , verbose = 0 ) :
'''Follows the solution path to find the best lambda value .''' | self . u = np . zeros ( self . Dk . shape [ 0 ] , dtype = 'double' )
lambda_grid = np . exp ( np . linspace ( np . log ( max_lambda ) , np . log ( min_lambda ) , lambda_bins ) )
aic_trace = np . zeros ( lambda_grid . shape )
# The AIC score for each lambda value
aicc_trace = np . zeros ( lambda_grid . shape )
# The AIC... |
def _calc_percent_disk_stats ( self , stats ) :
"""Calculate a percentage of used disk space for data and metadata""" | mtypes = [ 'data' , 'metadata' ]
percs = { }
for mtype in mtypes :
used = stats . get ( 'docker.{0}.used' . format ( mtype ) )
total = stats . get ( 'docker.{0}.total' . format ( mtype ) )
free = stats . get ( 'docker.{0}.free' . format ( mtype ) )
if used and total and free and ceil ( total ) < free + ... |
def create ( cls , name , servers = None , time_range = 'yesterday' , all_logs = False , filter_for_delete = None , comment = None , ** kwargs ) :
"""Create a new delete log task . Provide True to all _ logs to delete
all log types . Otherwise provide kwargs to specify each log by
type of interest .
: param s... | if not servers :
servers = [ svr . href for svr in ManagementServer . objects . all ( ) ]
servers . extend ( [ svr . href for svr in LogServer . objects . all ( ) ] )
else :
servers = [ svr . href for svr in servers ]
filter_for_delete = filter_for_delete . href if filter_for_delete else FilterExpression ( ... |
def recheck_limits ( self ) :
"""Re - check that the cached limits are the current limits .""" | limit_data = self . control_daemon . get_limits ( )
try : # Get the new checksum and list of limits
new_sum , new_limits = limit_data . get_limits ( self . limit_sum )
# Convert the limits list into a list of objects
lims = database . limits_hydrate ( self . db , new_limits )
# Save the new data
sel... |
def _rook_legal_for_castle ( self , rook ) :
"""Decides if given rook exists , is of this color , and has not moved so it
is eligible to castle .
: type : rook : Rook
: rtype : bool""" | return rook is not None and type ( rook ) is Rook and rook . color == self . color and not rook . has_moved |
def to_dataframe ( self , extra_edges_columns = [ ] ) :
"""Return this network in pandas DataFrame .
: return : Network as DataFrame . This is equivalent to SIF .""" | return df_util . to_dataframe ( self . session . get ( self . __url ) . json ( ) , edges_attr_cols = extra_edges_columns ) |
def connect_predecessors ( self , predecessors ) :
"""Connect all nodes in predecessors to this node .""" | for n in predecessors :
self . ingoing . append ( n )
n . outgoing . append ( self ) |
def clear_file_systems ( self ) :
"""Remove references to build and source file systems , reverting to the defaults""" | self . _source_url = None
self . dataset . config . library . source . url = None
self . _source_fs = None
self . _build_url = None
self . dataset . config . library . build . url = None
self . _build_fs = None
self . dataset . commit ( ) |
def device_query_retrieve ( self , query_id , ** kwargs ) : # noqa : E501
"""Retrieve a device query . # noqa : E501
Retrieve a specific device query . # noqa : E501
This method makes a synchronous HTTP request by default . To make an
asynchronous HTTP request , please pass asynchronous = True
> > > thread ... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'asynchronous' ) :
return self . device_query_retrieve_with_http_info ( query_id , ** kwargs )
# noqa : E501
else :
( data ) = self . device_query_retrieve_with_http_info ( query_id , ** kwargs )
# noqa : E501
return data |
def policy_parameters ( self ) :
"""Parameters of policy""" | return it . chain ( self . policy_backbone . parameters ( ) , self . action_head . parameters ( ) ) |
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