signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def unmount_loopbacks ( self ) :
"""Unmounts all loopback devices as identified by : func : ` find _ loopbacks `""" | # re - index loopback devices
self . _index_loopbacks ( )
for dev in self . find_loopbacks ( ) :
_util . check_output_ ( [ 'losetup' , '-d' , dev ] ) |
def by_id ( cls , oid ) :
"""Find a model object by its ` ` ObjectId ` ` ,
` ` oid ` ` can be string or ObjectId""" | if oid :
d = cls . collection . find_one ( ObjectId ( oid ) )
if d :
return cls ( ** d ) |
def makeHistory ( self ) :
'''Runs a loop of sow - - > cultivate - - > reap - - > mill act _ T times , tracking the
evolution of variables X named in track _ vars in attributes named X _ hist .
Parameters
none
Returns
none''' | self . reset ( )
# Initialize the state of the market
for t in range ( self . act_T ) :
self . sow ( )
# Distribute aggregated information / state to agents
self . cultivate ( )
# Agents take action
self . reap ( )
# Collect individual data from agents
self . mill ( )
# Process individua... |
def _heapqmergesorted ( key = None , * iterables ) :
"""Return a single iterator over the given iterables , sorted by the
given ` key ` function , assuming the input iterables are already sorted by
the same function . ( I . e . , the merge part of a general merge sort . ) Uses
: func : ` heapq . merge ` for t... | if key is None :
keyed_iterables = iterables
for element in heapq . merge ( * keyed_iterables ) :
yield element
else :
keyed_iterables = [ ( _Keyed ( key ( obj ) , obj ) for obj in iterable ) for iterable in iterables ]
for element in heapq . merge ( * keyed_iterables ) :
yield element .... |
def load ( self , data ) :
"""Load a single row of data and convert it into entities and
relations .""" | objs = { }
for mapper in self . entities :
objs [ mapper . name ] = mapper . load ( self . loader , data )
for mapper in self . relations :
objs [ mapper . name ] = mapper . load ( self . loader , data , objs ) |
def volume_create ( name , size = 100 , snapshot = None , voltype = None , ** kwargs ) :
'''Create block storage device''' | conn = get_conn ( )
create_kwargs = { 'name' : name , 'size' : size , 'snapshot' : snapshot , 'voltype' : voltype }
create_kwargs [ 'availability_zone' ] = kwargs . get ( 'availability_zone' , None )
return conn . volume_create ( ** create_kwargs ) |
def read_config_file ( f ) :
"""Read a config file .""" | if isinstance ( f , basestring ) :
f = os . path . expanduser ( f )
try :
config = ConfigObj ( f , interpolation = False , encoding = 'utf8' )
except ConfigObjError as e :
log ( LOGGER , logging . ERROR , "Unable to parse line {0} of config file " "'{1}'." . format ( e . line_number , f ) )
log ( LOGGER... |
def get_axis_variables ( ds ) :
'''Returns a list of variables that define an axis of the dataset
: param netCDF4 . Dataset ds : An open netCDF4 Dataset''' | axis_variables = [ ]
for ncvar in ds . get_variables_by_attributes ( axis = lambda x : x is not None ) :
axis_variables . append ( ncvar . name )
return axis_variables |
def get_question ( self , assessment_section_id , item_id ) :
"""Gets the ` ` Question ` ` specified by its ` ` Id ` ` .
arg : assessment _ section _ id ( osid . id . Id ) : ` ` Id ` ` of the
` ` AssessmentSection ` `
arg : item _ id ( osid . id . Id ) : ` ` Id ` ` of the ` ` Item ` `
return : ( osid . asse... | return self . get_assessment_section ( assessment_section_id ) . get_question ( question_id = item_id ) |
def to_dict_list ( df , use_ordered_dict = True ) :
"""Transform each row to dict , and put them into a list .
* * 中文文档 * *
将 ` ` pandas . DataFrame ` ` 转换成一个字典的列表 。 列表的长度与行数相同 , 其中
每一个字典相当于表中的一行 , 相当于一个 ` ` pandas . Series ` ` 对象 。""" | if use_ordered_dict :
dict = OrderedDict
columns = df . columns
data = list ( )
for tp in itertuple ( df ) :
data . append ( dict ( zip ( columns , tp ) ) )
return data |
def optimize ( self , commit = True , waitFlush = None , waitSearcher = None , maxSegments = None , handler = 'update' ) :
"""Tells Solr to streamline the number of segments used , essentially a
defragmentation operation .
Optionally accepts ` ` maxSegments ` ` . Default is ` ` None ` ` .
Optionally accepts `... | if maxSegments :
msg = '<optimize maxSegments="%d" />' % maxSegments
else :
msg = '<optimize />'
return self . _update ( msg , commit = commit , waitFlush = waitFlush , waitSearcher = waitSearcher , handler = handler ) |
def _zeep_to_dict ( cls , obj ) :
"""Convert a zeep object to a dictionary .""" | res = serialize_object ( obj )
res = cls . _get_non_empty_dict ( res )
return res |
def escape_vals ( vals , escape_numerics = True ) :
"""Escapes a list of values to a string , converting to
unicode for safety .""" | # Ints formatted as floats to disambiguate with counter mode
ints , floats = "%.1f" , "%.10f"
escaped = [ ]
for v in vals :
if isinstance ( v , np . timedelta64 ) :
v = "'" + str ( v ) + "'"
elif isinstance ( v , np . datetime64 ) :
v = "'" + str ( v . astype ( 'datetime64[ns]' ) ) + "'"
eli... |
def unpack_kraus_matrix ( m ) :
"""Helper to optionally unpack a JSON compatible representation of a complex Kraus matrix .
: param Union [ list , np . array ] m : The representation of a Kraus operator . Either a complex
square matrix ( as numpy array or nested lists ) or a JSON - able pair of real matrices
... | m = np . asarray ( m , dtype = complex )
if m . ndim == 3 :
m = m [ 0 ] + 1j * m [ 1 ]
if not m . ndim == 2 : # pragma no coverage
raise ValueError ( "Need 2d array." )
if not m . shape [ 0 ] == m . shape [ 1 ] : # pragma no coverage
raise ValueError ( "Need square matrix." )
return m |
def _isomorphism_rewrite_to_NECtree ( q_s , qgraph ) :
"""Neighborhood Equivalence Class tree ( see Turbo _ ISO paper )""" | qadj = qgraph . adj
adjsets = lambda x : set ( chain . from_iterable ( qadj [ x ] . values ( ) ) )
t = ( [ q_s ] , [ ] )
# ( NEC _ set , children )
visited = { q_s }
vcur , vnext = [ t ] , [ ]
while vcur :
for ( nec , children ) in vcur :
c = defaultdict ( list )
for u in nec :
for sig ,... |
def plot_wfdb ( record = None , annotation = None , plot_sym = False , time_units = 'samples' , title = None , sig_style = [ '' ] , ann_style = [ 'r*' ] , ecg_grids = [ ] , figsize = None , return_fig = False ) :
"""Subplot individual channels of a wfdb record and / or annotation .
This function implements the ba... | ( signal , ann_samp , ann_sym , fs , ylabel , record_name ) = get_wfdb_plot_items ( record = record , annotation = annotation , plot_sym = plot_sym )
return plot_items ( signal = signal , ann_samp = ann_samp , ann_sym = ann_sym , fs = fs , time_units = time_units , ylabel = ylabel , title = ( title or record_name ) , s... |
def read_string_data ( file , number_values , endianness ) :
"""Read string raw data
This is stored as an array of offsets
followed by the contiguous string data .""" | offsets = [ 0 ]
for i in range ( number_values ) :
offsets . append ( types . Uint32 . read ( file , endianness ) )
strings = [ ]
for i in range ( number_values ) :
s = file . read ( offsets [ i + 1 ] - offsets [ i ] )
strings . append ( s . decode ( 'utf-8' ) )
return strings |
def login ( self , action , registry , ** kwargs ) :
"""Logs in to a Docker registry .
: param action : Action configuration .
: type action : dockermap . map . runner . ActionConfig
: param registry : Name of the registry server to login to .
: type registry : unicode | str
: param kwargs : Additional ke... | log . info ( "Logging into registry %s." , registry )
login_kwargs = { 'registry' : registry }
auth_config = action . client_config . auth_configs . get ( registry )
if auth_config :
log . debug ( "Registry auth config for %s found." , registry )
login_kwargs . update ( auth_config )
insecure_registry = kwa... |
def agg ( self , aggregations ) :
"""Multiple aggregations optimized .
Parameters
aggregations : list of str
Which aggregations to perform .
Returns
Series
Series with resulting aggregations .""" | check_type ( aggregations , list )
new_index = Index ( np . array ( aggregations , dtype = np . bytes_ ) , np . dtype ( np . bytes_ ) )
return _series_agg ( self , aggregations , new_index ) |
def iter_chat_members ( self , chat_id : Union [ int , str ] , limit : int = 0 , query : str = "" , filter : str = Filters . ALL ) -> Generator [ "pyrogram.ChatMember" , None , None ] :
"""Use this method to iterate through the members of a chat sequentially .
This convenience method does the same as repeatedly c... | current = 0
yielded = set ( )
queries = [ query ] if query else QUERIES
total = limit or ( 1 << 31 ) - 1
limit = min ( 200 , total )
resolved_chat_id = self . resolve_peer ( chat_id )
filter = ( Filters . RECENT if self . get_chat_members_count ( chat_id ) <= 10000 and filter == Filters . ALL else filter )
if filter no... |
def apply ( coro , * args , ** kw ) :
"""Creates a continuation coroutine function with some arguments
already applied .
Useful as a shorthand when combined with other control flow functions .
Any arguments passed to the returned function are added to the arguments
originally passed to apply .
This is sim... | assert_corofunction ( coro = coro )
@ asyncio . coroutine
def wrapper ( * _args , ** _kw ) : # Explicitely ignore wrapper arguments
return ( yield from coro ( * args , ** kw ) )
return wrapper |
def open ( self , filename = None ) :
'''Open a browser tab with the notebook path specified relative to the
notebook directory .
If no filename is specified , open the root of the notebook server .''' | if filename is None :
address = self . address + 'tree'
else :
notebook_path = self . resource_filename ( filename )
if not notebook_path . isfile ( ) :
raise IOError ( 'Notebook path not found: %s' % notebook_path )
else :
address = '%snotebooks/%s' % ( self . address , filename )
webbr... |
def public_key_sec ( self ) :
"""Return the public key as sec , or None in case of failure .""" | if self . is_coinbase ( ) :
return None
opcodes = ScriptTools . opcode_list ( self . script )
if len ( opcodes ) == 2 and opcodes [ 0 ] . startswith ( "[30" ) : # the second opcode is probably the public key as sec
sec = h2b ( opcodes [ 1 ] [ 1 : - 1 ] )
return sec
return None |
def change_subpage ( self , offset = None , max_page_count = None , nom = True ) :
"""Args :
* offset - Integer - The positive / negative change to apply
to the page .
* max _ page _ count - The maximum number of pages available .
* nom - None on Max or Min - If max number of pages reached ,
return none i... | if offset == None :
return
if self . slots [ 'subpage' ] == None :
self . slots [ 'subpage' ] = 1
if ( self . slots [ 'subpage' ] + offset > max_page_count ) and nom :
return None
elif ( self . slots [ 'subpage' ] + offset < 1 ) and nom :
return None
else :
self . slots [ 'subpage' ] = norm_page_cnt... |
def _reverse_problem_hparams ( p_hparams ) :
"""Swap input / output modalities , vocab , and space ids .""" | p = p_hparams
# Swap modalities .
# TODO ( trandustin ) : Note this assumes target modalities have feature name
# ' target ' , and each intended feature to swap has feature name ' input ' .
# In the future , remove need for this behavior .
reversed_modality = { }
for feature_name in p . modality :
reversed_feature_... |
def define_models ( self , ic , leaves = None , N = 1 , index = 0 ) :
"""N , index are either integers or lists of integers .
N : number of model stars per observed star
index : index of physical association
leaves : either a list of leaves , or a pattern by which
the leaves are selected ( via ` select _ le... | self . clear_models ( )
if leaves is None :
leaves = self . _get_leaves ( )
elif type ( leaves ) == type ( '' ) :
leaves = self . select_leaves ( leaves )
# Sort leaves by distance , to ensure system 0 will be assigned
# to the main reference star .
if np . isscalar ( N ) :
N = ( np . ones ( len ( leaves ) ... |
def blacklist_bulk ( self , blacklist ) :
"""Add blacklist entries to the engine node in bulk . For blacklist to work ,
you must also create a rule with action " Apply Blacklist " .
First create your blacklist entries using : class : ` smc . elements . other . Blacklist `
then provide the blacklist to this me... | self . make_request ( EngineCommandFailed , method = 'create' , resource = 'blacklist' , json = blacklist . entries ) |
def import_from_hdf5 ( network , path , skip_time = False ) :
"""Import network data from HDF5 store at ` path ` .
Parameters
path : string
Name of HDF5 store
skip _ time : bool , default False
Skip reading in time dependent attributes""" | basename = os . path . basename ( path )
with ImporterHDF5 ( path ) as importer :
_import_from_importer ( network , importer , basename = basename , skip_time = skip_time ) |
def get_facet_serializer ( self , * args , ** kwargs ) :
"""Return the facet serializer instance that should be used for
serializing faceted output .""" | assert "objects" in kwargs , "`objects` is a required argument to `get_facet_serializer()`"
facet_serializer_class = self . get_facet_serializer_class ( )
kwargs [ "context" ] = self . get_serializer_context ( )
kwargs [ "context" ] . update ( { "objects" : kwargs . pop ( "objects" ) , "facet_query_params_text" : self ... |
def can_update_assets ( self ) :
"""Tests if this user can update ` ` Assets ` ` .
A return of true does not guarantee successful authorization . A
return of false indicates that it is known updating an ` ` Asset ` `
will result in a ` ` PermissionDenied ` ` . This is intended as a
hint to an application th... | url_path = construct_url ( 'authorization' , bank_id = self . _catalog_idstr )
return self . _get_request ( url_path ) [ 'assetHints' ] [ 'canUpdate' ] |
def start_root_token_generation ( self , otp = None , pgp_key = None ) :
"""Initialize a new root generation attempt .
Only a single root generation attempt can take place at a time . One ( and only one ) of otp or pgp _ key are
required .
Supported methods :
PUT : / sys / generate - root / attempt . Produc... | params = { }
if otp is not None and pgp_key is not None :
raise ParamValidationError ( 'one (and only one) of otp or pgp_key arguments are required' )
if otp is not None :
params [ 'otp' ] = otp
if pgp_key is not None :
params [ 'pgp_key' ] = pgp_key
api_path = '/v1/sys/generate-root/attempt'
response = sel... |
def _get_float_remainder ( fvalue , signs = 9 ) :
"""Get remainder of float , i . e . 2.05 - > ' 05'
@ param fvalue : input value
@ type fvalue : C { integer types } , C { float } or C { Decimal }
@ param signs : maximum number of signs
@ type signs : C { integer types }
@ return : remainder
@ rtype : C... | check_positive ( fvalue )
if isinstance ( fvalue , six . integer_types ) :
return "0"
if isinstance ( fvalue , Decimal ) and fvalue . as_tuple ( ) [ 2 ] == 0 : # Decimal . as _ tuple ( ) - > ( sign , digit _ tuple , exponent )
# если экспонента " 0 " - - значит дробной части нет
return "0"
signs = min ( signs ... |
def drag_and_drop_by_offset ( self , source , xoffset , yoffset ) :
"""Holds down the left mouse button on the source element ,
then moves to the target offset and releases the mouse button .
: Args :
- source : The element to mouse down .
- xoffset : X offset to move to .
- yoffset : Y offset to move to ... | self . click_and_hold ( source )
self . move_by_offset ( xoffset , yoffset )
self . release ( )
return self |
def update_timestep ( self , modelparams , expparams ) :
r"""Returns a set of model parameter vectors that is the update of an
input set of model parameter vectors , such that the new models are
conditioned on a particular experiment having been performed .
By default , this is the trivial function
: math :... | return np . tile ( modelparams , ( expparams . shape [ 0 ] , 1 , 1 ) ) . transpose ( ( 1 , 2 , 0 ) ) |
def stdout ( self ) :
"""Флаг - - stdout может быть взят из переменной окружения CROSSPM _ STDOUT .
Если есть любое значение в CROSSPM _ STDOUT - оно понимается как True
: return :""" | # - - stdout
stdout = self . _args [ '--stdout' ]
if stdout :
return True
# CROSSPM _ STDOUT
stdout_env = os . getenv ( 'CROSSPM_STDOUT' , None )
if stdout_env is not None :
return True
return False |
def GetDateRange ( self ) :
"""Return the range over which this ServicePeriod is valid .
The range includes exception dates that add service outside of
( start _ date , end _ date ) , but doesn ' t shrink the range if exception
dates take away service at the edges of the range .
Returns :
A tuple of " YYY... | start = self . start_date
end = self . end_date
for date , ( exception_type , _ ) in self . date_exceptions . items ( ) :
if exception_type == self . _EXCEPTION_TYPE_REMOVE :
continue
if not start or ( date < start ) :
start = date
if not end or ( date > end ) :
end = date
if start i... |
def _getCharWidths ( self , xref , bfname , ext , ordering , limit , idx = 0 ) :
"""Return list of glyphs and glyph widths of a font .""" | if self . isClosed or self . isEncrypted :
raise ValueError ( "operation illegal for closed / encrypted doc" )
return _fitz . Document__getCharWidths ( self , xref , bfname , ext , ordering , limit , idx ) |
def get_cursor_right_position ( self , count = 1 ) :
"""Relative position for cursor _ right .""" | if count < 0 :
return self . get_cursor_left_position ( - count )
return min ( count , len ( self . current_line_after_cursor ) ) |
def fetch_next_page ( self ) :
"""Manually , synchronously fetch the next page . Supplied for manually retrieving pages
and inspecting : meth : ` ~ . current _ page ` . It is not necessary to call this when iterating
through results ; paging happens implicitly in iteration .""" | if self . response_future . has_more_pages :
self . response_future . start_fetching_next_page ( )
result = self . response_future . result ( )
self . _current_rows = result . _current_rows
# ResultSet has already _ set _ current _ rows to the appropriate form
else :
self . _current_rows = [ ] |
def write_dataframe ( rows , encoding = ENCODING , dialect = DIALECT , ** kwargs ) :
"""Dump ` ` rows ` ` to string buffer and load with ` ` pandas . read _ csv ( ) ` ` using ` ` kwargs ` ` .""" | global pandas
if pandas is None : # pragma : no cover
import pandas
with contextlib . closing ( CsvBuffer ( ) ) as fd :
write_csv ( fd , rows , encoding , dialect )
fd . seek ( 0 )
df = read_csv ( pandas , fd , encoding , dialect , kwargs )
return df |
def add_highlight_area ( self , mask , label = None , col = 0 ) :
"""add a highlighted area - - outline an arbitrarily shape - -
as if drawn from a Lasso event .
This takes a mask , which should be a boolean array of the
same shape as the image .""" | patch = mask * np . ones ( mask . shape ) * 0.9
cmap = self . conf . cmap [ col ]
area = self . axes . contour ( patch , cmap = cmap , levels = [ 0 , 1 ] )
self . conf . highlight_areas . append ( area )
col = None
if hasattr ( cmap , '_lut' ) :
rgb = [ int ( i * 240 ) ^ 255 for i in cmap . _lut [ 0 ] [ : 3 ] ]
... |
def predict_in_frame_coding_effect ( variant , transcript , trimmed_cdna_ref , trimmed_cdna_alt , sequence_from_start_codon , cds_offset ) :
"""Coding effect of an in - frame nucleotide change
Parameters
variant : Variant
transcript : Transcript
trimmed _ cdna _ ref : str
Reference nucleotides from the co... | ref_codon_start_offset , ref_codon_end_offset , mutant_codons = get_codons ( variant = variant , trimmed_cdna_ref = trimmed_cdna_ref , trimmed_cdna_alt = trimmed_cdna_alt , sequence_from_start_codon = sequence_from_start_codon , cds_offset = cds_offset )
mutation_affects_start_codon = ( ref_codon_start_offset == 0 )
if... |
def save_xml ( self , doc , element ) :
'''Save this execution context into an xml . dom . Element object .''' | element . setAttributeNS ( XSI_NS , XSI_NS_S + 'type' , 'rtsExt:execution_context_ext' )
element . setAttributeNS ( RTS_NS , RTS_NS_S + 'id' , self . id )
element . setAttributeNS ( RTS_NS , RTS_NS_S + 'kind' , self . kind )
element . setAttributeNS ( RTS_NS , RTS_NS_S + 'rate' , str ( self . rate ) )
for p in self . p... |
def orng_type ( self , table_name , col ) :
'''Returns an Orange datatype for a given mysql column .
: param table _ name : target table name
: param col : column to determine the Orange datatype''' | mysql_type = self . types [ table_name ] [ col ]
n_vals = len ( self . db . col_vals [ table_name ] [ col ] )
if mysql_type in OrangeConverter . continuous_types or ( n_vals >= 50 and mysql_type in OrangeConverter . integer_types ) :
return 'c'
elif mysql_type in OrangeConverter . ordinal_types + OrangeConverter . ... |
def _parse_status ( data , cast_type ) :
"""Parses a STATUS message and returns a CastStatus object .
: type data : dict
: param cast _ type : Type of Chromecast .
: rtype : CastStatus""" | data = data . get ( 'status' , { } )
volume_data = data . get ( 'volume' , { } )
try :
app_data = data [ 'applications' ] [ 0 ]
except KeyError :
app_data = { }
is_audio = cast_type in ( CAST_TYPE_AUDIO , CAST_TYPE_GROUP )
status = CastStatus ( data . get ( 'isActiveInput' , None if is_audio else False ) , data... |
def bed ( args ) :
"""% prog bed btabfile
Convert btab to bed format .""" | from jcvi . formats . blast import BlastLine
p = OptionParser ( bed . __doc__ )
opts , args = p . parse_args ( args )
if len ( args ) != 1 :
sys . exit ( not p . print_help ( ) )
btabfile , = args
btab = Btab ( btabfile )
for b in btab :
Bline = BlastLine ( b . blastline )
print ( Bline . bedline ) |
def package_assets ( example_path ) :
"""Generates pseudo - packages for the examples directory .""" | examples ( example_path , force = True , root = __file__ )
for root , dirs , files in os . walk ( example_path ) :
walker ( root , dirs + files )
setup_args [ 'packages' ] += packages
for p , exts in extensions . items ( ) :
if exts :
setup_args [ 'package_data' ] [ p ] = exts |
def jsLocal ( self , time_zone = '' ) :
'''a method to report a javascript string from a labDT object
: param time _ zone : [ optional ] string with timezone to report in
: return : string with date and time info''' | # validate inputs
js_format = '%a %b %d %Y %H:%M:%S GMT%z (%Z)'
title = 'Timezone input for labDT.jsLocal'
get_tz = get_localzone ( )
if time_zone : # if time _ zone . lower ( ) in ( ' utc ' , ' uct ' , ' universal ' , ' zulu ' ) :
# raise ValueError ( ' time _ zone cannot be UTC . % s requires a local timezone value .... |
def url ( self ) :
"""Returns the URL for the resource based on the ` ` self ` ` link .
This method returns the ` ` href ` ` of the document ' s ` ` self ` ` link if it
has one , or ` ` None ` ` if the document lacks a ` ` self ` ` link , or the
` ` href ` ` of the document ' s first ` ` self ` ` link if it h... | if not 'self' in self . links :
return None
self_link = self . links [ 'self' ]
if isinstance ( self_link , list ) :
for link in self_link :
return link . url ( )
return self_link . url ( ) |
def show_firmware_version_output_show_firmware_version_node_info_is_active_cp ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
show_firmware_version = ET . Element ( "show_firmware_version" )
config = show_firmware_version
output = ET . SubElement ( show_firmware_version , "output" )
show_firmware_version = ET . SubElement ( output , "show-firmware-version" )
node_info = ET . SubElement ( show_firmware_versio... |
def _get_unstack_items ( self , unstacker , new_columns ) :
"""Get the placement , values , and mask for a Block unstack .
This is shared between ObjectBlock and ExtensionBlock . They
differ in that ObjectBlock passes the values , while ExtensionBlock
passes the dummy ndarray of positions to be used by a take... | # shared with ExtensionBlock
new_items = unstacker . get_new_columns ( )
new_placement = new_columns . get_indexer ( new_items )
new_values , mask = unstacker . get_new_values ( )
mask = mask . any ( 0 )
return new_placement , new_values , mask |
def calc ( args ) :
"""% prog calc [ prot . fasta ] cds . fasta > out . ks
Protein file is optional . If only one file is given , it is assumed to
be CDS sequences with correct frame ( frame 0 ) . Results will be written to
stdout . Both protein file and nucleotide file are assumed to be Fasta format ,
with... | from jcvi . formats . fasta import translate
p = OptionParser ( calc . __doc__ )
p . add_option ( "--longest" , action = "store_true" , help = "Get longest ORF, only works if no pep file, " "e.g. ESTs [default: %default]" )
p . add_option ( "--msa" , default = "clustalw" , choices = ( "clustalw" , "muscle" ) , help = "... |
def export_go ( self , go_template = GO_TEMPLATE , go_indent = GO_INDENTATION , go_package = GO_PACKAGE ) :
'''Export the grammar to a Go file which can be
used with the goleri module .''' | language = [ ]
enums = set ( )
indent = 0
pattern = self . RE_KEYWORDS . pattern . replace ( '`' , '` + "`" + `' )
if not pattern . startswith ( '^' ) :
pattern = '^' + pattern
for name in self . _order :
elem = getattr ( self , name , None )
if not isinstance ( elem , Element ) :
continue
if no... |
def merge_attributes ( attr1 , attr2 ) :
"""Merges two attribute dictionaries into a single dictionary .
Parameters
` attr1 ` , ` attr2 ` : dict
Returns
dict""" | new_d = copy . deepcopy ( attr1 )
new_d . update ( attr2 )
# all of attr2 key : values just overwrote attr1 , fix it
for k , v in new_d . items ( ) :
if not isinstance ( v , list ) :
new_d [ k ] = [ v ]
for k , v in six . iteritems ( attr1 ) :
if k in attr2 :
if not isinstance ( v , list ) :
... |
def _calculate_block_structure ( self , inequalities , equalities , momentinequalities , momentequalities , extramomentmatrix , removeequalities , block_struct = None ) :
"""Calculates the block _ struct array for the output file .""" | block_struct = [ ]
if self . verbose > 0 :
print ( "Calculating block structure..." )
block_struct . append ( len ( self . monomial_sets [ 0 ] ) * len ( self . monomial_sets [ 1 ] ) )
if extramomentmatrix is not None :
for _ in extramomentmatrix :
block_struct . append ( len ( self . monomial_sets [ 0 ]... |
def read_filepath ( filepath , encoding = 'utf-8' ) :
"""Returns the text content of ` filepath `""" | with codecs . open ( filepath , 'r' , encoding = encoding ) as fo :
return fo . read ( ) |
def _assert_safe_casting ( cls , data , subarr ) :
"""Ensure incoming data can be represented as ints .""" | if not issubclass ( data . dtype . type , np . signedinteger ) :
if not np . array_equal ( data , subarr ) :
raise TypeError ( 'Unsafe NumPy casting, you must ' 'explicitly cast' ) |
def simplify_compound_subjects ( sentence_str ) :
"""Given a sentence doc , return a new sentence doc with compound subjects
reduced to their simplest forms .
' The man , the boy , and the girl went to school . '
would reduce to ' They went to school '
' The man , the boy , or the girls are frauds . '
wou... | sentence_doc = textacy . Doc ( sentence_str , lang = 'en_core_web_lg' )
cs_patterns = [ r'((<DET>?(<NOUN|PROPN>|<PRON>)+<PUNCT>)+<DET>?(<NOUN|PROPN>|<PRON>)+<PUNCT>?<CCONJ><DET>?(<NOUN|PROPN>|<PRON>)+)|' '(<DET>?(<NOUN|PROPN>|<PRON>)<CCONJ><DET>?(<NOUN|PROPN>|<PRON>))' ]
for cs_pattern in cs_patterns :
compound_sub... |
def authn_request ( self , context , entity_id ) :
"""Do an authorization request on idp with given entity id .
This is the start of the authorization .
: type context : satosa . context . Context
: type entity _ id : str
: rtype : satosa . response . Response
: param context : The current context
: par... | # If IDP blacklisting is enabled and the selected IDP is blacklisted ,
# stop here
if self . idp_blacklist_file :
with open ( self . idp_blacklist_file ) as blacklist_file :
blacklist_array = json . load ( blacklist_file ) [ 'blacklist' ]
if entity_id in blacklist_array :
satosa_logging ... |
def set_computed_cost_arr ( self , value ) :
'''setter''' | if isinstance ( value , np . ndarray ) :
self . __computed_cost_arr = value
else :
raise TypeError ( ) |
def repair ( self , volume_id_or_uri , timeout = - 1 ) :
"""Removes extra presentations from a specified volume on the storage system .
Args :
volume _ id _ or _ uri :
Can be either the volume id or the volume uri .
timeout :
Timeout in seconds . Wait for task completion by default . The timeout does not ... | data = { "type" : "ExtraManagedStorageVolumePaths" , "resourceUri" : self . _client . build_uri ( volume_id_or_uri ) }
custom_headers = { 'Accept-Language' : 'en_US' }
uri = self . URI + '/repair'
return self . _client . create ( data , uri = uri , timeout = timeout , custom_headers = custom_headers ) |
def expectation_payload ( prep_prog , operator_programs , random_seed ) :
"""REST payload for : py : func : ` ForestConnection . _ expectation `""" | if operator_programs is None :
operator_programs = [ Program ( ) ]
if not isinstance ( prep_prog , Program ) :
raise TypeError ( "prep_prog variable must be a Quil program object" )
payload = { 'type' : TYPE_EXPECTATION , 'state-preparation' : prep_prog . out ( ) , 'operators' : [ x . out ( ) for x in operator_... |
def autoencoder_discrete_cifar ( ) :
"""Discrete autoencoder model for compressing cifar .""" | hparams = autoencoder_ordered_discrete ( )
hparams . bottleneck_noise = 0.0
hparams . bottleneck_bits = 90
hparams . num_hidden_layers = 2
hparams . hidden_size = 256
hparams . num_residual_layers = 4
hparams . batch_size = 32
hparams . learning_rate_constant = 1.0
return hparams |
def generate_username ( self , user_class ) :
"""Generate a new username for a user""" | m = getattr ( user_class , 'generate_username' , None )
if m :
return m ( )
else :
max_length = user_class . _meta . get_field ( self . username_field ) . max_length
return uuid . uuid4 ( ) . hex [ : max_length ] |
def strict_dependencies ( self , dep_context ) :
""": param dep _ context : A DependencyContext with configuration for the request .
: return : targets that this target " strictly " depends on . This set of dependencies contains
only directly declared dependencies , with two exceptions :
1 ) aliases are expan... | strict_deps = self . _cached_strict_dependencies_map . get ( dep_context , None )
if strict_deps is None :
default_predicate = self . _closure_dep_predicate ( { self } , ** dep_context . target_closure_kwargs )
# TODO ( # 5977 ) : this branch needs testing !
if not default_predicate :
def default_pr... |
def watch ( logger_name , level = DEBUG , out = stdout ) :
"""Quick wrapper for using the Watcher .
: param logger _ name : name of logger to watch
: param level : minimum log level to show ( default INFO )
: param out : where to send output ( default stdout )
: return : Watcher instance""" | watcher = Watcher ( logger_name )
watcher . watch ( level , out )
return watcher |
def concat_urls ( * urls ) :
"""Concat Urls
Args :
* args : ( str )
Returns :
str : urls starting and ending with / merged with /""" | normalized_urls = filter ( bool , [ url . strip ( '/' ) for url in urls ] )
joined_urls = '/' . join ( normalized_urls )
if not joined_urls :
return '/'
return '/{}/' . format ( joined_urls ) |
def matrix ( self , x = ( 0 , 0 ) , y = ( 0 , 0 ) , z = ( 0 , 0 ) ) :
"""Copy the ` ` pyny . Polygon ` ` along a 3D matrix given by the
three tuples x , y , z :
: param x : Number of copies and distance between them in this
direction .
: type x : tuple ( len = 2)
: returns : list of ` ` pyny . Polygons ` ... | space = Space ( Place ( Surface ( self ) ) )
space = space . matrix ( x , y , z , inplace = False )
return [ place . surface [ 0 ] for place in space ] |
def stop ( self ) :
"""stops the process triggered by start
Setting the shared memory boolean run to false , which should prevent
the loop from repeating . Call _ _ cleanup to make sure the process
stopped . After that we could trigger start ( ) again .""" | if self . is_alive ( ) :
self . _proc . terminate ( )
if self . _proc is not None :
self . __cleanup ( )
if self . raise_error :
if self . _proc . exitcode == 255 :
raise LoopExceptionError ( "the loop function return non zero exticode ({})!\n" . format ( self . _proc . exitcode ) + "see... |
def _setup_maya ( ) :
"""Setup Maya logging , but be * really * defensive about it .""" | # We are having trouble with this in Mark Media . For some reason this
# remains importable from a uifutures . host launched from Maya .
return
try :
import maya . utils
except ImportError :
return
# Remove the shell handler ; we have created one ourselves .
if hasattr ( maya . utils , 'shellLogHandler' ) :
... |
def get_yarn_applications ( self , start_time , end_time , filter_str = "" , limit = 100 , offset = 0 ) :
"""Returns a list of YARN applications that satisfy the filter
@ type start _ time : datetime . datetime . Note that the datetime must either be
time zone aware or specified in the server time zone . See
... | params = { 'from' : start_time . isoformat ( ) , 'to' : end_time . isoformat ( ) , 'filter' : filter_str , 'limit' : limit , 'offset' : offset }
return self . _get ( "yarnApplications" , ApiYarnApplicationResponse , params = params , api_version = 6 ) |
def device_selected ( self , index ) :
"""Handler for selecting a device from the list in the UI""" | device = self . devicelist_model . itemFromIndex ( index )
print ( device . device . addr )
self . btnConnect . setEnabled ( True ) |
def sanitize_qualifiers ( repos = None , followers = None , language = None ) :
'''qualifiers = c repos : + 42 followers : + 1000 language :
params = { ' q ' : ' tom repos : > 42 followers : > 1000 ' }''' | qualifiers = ''
if repos :
qualifiers += 'repos:{0} ' . format ( repos )
qualifiers = re . sub ( r"([+])([=a-zA-Z0-9]+)" , r">\2" , qualifiers )
qualifiers = re . sub ( r"([-])([=a-zA-Z0-9]+)" , r"<\2" , qualifiers )
if followers :
qualifiers += 'followers:{0} ' . format ( followers )
qualifiers = r... |
def process_task ( self ) :
"""This function is called when the client has failed to send all of the
segments of a segmented request , the application has taken too long to
complete the request , or the client failed to ack the segments of a
segmented response .""" | if _debug :
ServerSSM . _debug ( "process_task" )
if self . state == SEGMENTED_REQUEST :
self . segmented_request_timeout ( )
elif self . state == AWAIT_RESPONSE :
self . await_response_timeout ( )
elif self . state == SEGMENTED_RESPONSE :
self . segmented_response_timeout ( )
elif self . state == COMPL... |
def instance_default ( self , obj ) :
'''Get the default value that will be used for a specific instance .
Args :
obj ( HasProps ) : The instance to get the default value for .
Returns :
object''' | return self . property . themed_default ( obj . __class__ , self . name , obj . themed_values ( ) ) |
def setattrdeep ( obj , attr , val ) :
'Set dotted attr ( like " a . b . c " ) on obj to val .' | attrs = attr . split ( '.' )
for a in attrs [ : - 1 ] :
obj = getattr ( obj , a )
setattr ( obj , attrs [ - 1 ] , val ) |
def delete_repo ( self , repo_name = None , envs = [ ] , query = '/repositories/' ) :
"""` repo _ name ` - Name of repository to delete
Delete repo in specified environments""" | orphan_query = '/content/orphans/rpm/'
juicer . utils . Log . log_debug ( "Delete Repo: %s" , repo_name )
for env in self . args . envs :
if not juicer . utils . repo_exists_p ( repo_name , self . connectors [ env ] , env ) :
juicer . utils . Log . log_info ( "repo `%s` doesn't exist in %s... skipping!" , (... |
def InputCodon ( seq_length , ignore_stop_codons = True , name = None , ** kwargs ) :
"""Input placeholder for array returned by ` encodeCodon `
Note : The seq _ length is divided by 3
Wrapper for : ` keras . layers . Input ( ( seq _ length / 3 , 61 or 61 ) , name = name , * * kwargs ) `""" | if ignore_stop_codons :
vocab = CODONS
else :
vocab = CODONS + STOP_CODONS
assert seq_length % 3 == 0
return Input ( ( seq_length / 3 , len ( vocab ) ) , name = name , ** kwargs ) |
def after_each_callback ( eng , callback_func , obj ) :
"""Take action after every WF callback .""" | obj . callback_pos = eng . state . callback_pos
obj . extra_data [ "_last_task_name" ] = callback_func . __name__
task_history = get_task_history ( callback_func )
if "_task_history" not in obj . extra_data :
obj . extra_data [ "_task_history" ] = [ task_history ]
else :
obj . extra_data [ "_task_history" ] . a... |
def SpinBasisKet ( * numer_denom , hs ) :
"""Constructor for a : class : ` BasisKet ` for a : class : ` SpinSpace `
For a half - integer spin system : :
> > > hs = SpinSpace ( ' s ' , spin = ( 3 , 2 ) )
> > > assert SpinBasisKet ( 1 , 2 , hs = hs ) = = BasisKet ( " + 1/2 " , hs = hs )
For an integer spin sy... | try :
spin_numer , spin_denom = hs . spin . as_numer_denom ( )
except AttributeError :
raise TypeError ( "hs=%s for SpinBasisKet must be a SpinSpace instance" % hs )
assert spin_denom in ( 1 , 2 )
if spin_denom == 1 : # integer spin
if len ( numer_denom ) != 1 :
raise TypeError ( "SpinBasisKet requi... |
def _throttle_error ( self , msg , * args , ** kwargs ) :
"""Avoids sending errors repeatedly . Waits at least
` self . server _ error _ interval ` seconds before sending the same error
string to the error logging facility . If not enough time has passed ,
it calls ` log . debug ` instead
Receives the same ... | now = time . time ( )
if msg in self . _errors :
if ( ( now - self . _errors [ msg ] ) >= self . server_error_interval ) :
fn = self . log . error
self . _errors [ msg ] = now
else :
fn = self . log . debug
else :
self . _errors [ msg ] = now
fn = self . log . error
return fn ( m... |
def _construct_X ( self , omega , weighted = True , ** kwargs ) :
"""Construct the design matrix for the problem""" | t = kwargs . get ( 't' , self . t )
dy = kwargs . get ( 'dy' , self . dy )
fit_offset = kwargs . get ( 'fit_offset' , self . fit_offset )
if fit_offset :
offsets = [ np . ones ( len ( t ) ) ]
else :
offsets = [ ]
cols = sum ( ( [ np . sin ( ( i + 1 ) * omega * t ) , np . cos ( ( i + 1 ) * omega * t ) ] for i in... |
async def flush ( self , request : Request , stacks : List [ Stack ] ) :
"""Add a typing stack after each stack .""" | ns : List [ Stack ] = [ ]
for stack in stacks :
ns . extend ( self . typify ( stack ) )
if len ( ns ) > 1 and ns [ - 1 ] == Stack ( [ lyr . Typing ( ) ] ) :
ns [ - 1 ] . get_layer ( lyr . Typing ) . active = False
await self . next ( request , ns ) |
def removecontains ( args ) :
"""% prog removecontains 4 - unitigger / best . contains asm . gkpStore
Remove contained reads from gkpStore . This will improve assembly contiguity
without sacrificing accuracy , when using bogart unitigger .""" | p = OptionParser ( removecontains . __doc__ )
opts , args = p . parse_args ( args )
if len ( args ) != 2 :
sys . exit ( not p . print_help ( ) )
contains , gkpStore = args
s = set ( )
fp = open ( contains )
for row in fp :
if row [ 0 ] == '#' :
continue
iid = int ( row . split ( ) [ 0 ] )
s . ad... |
def nb_persons ( self , role = None ) :
"""Returns the number of persons contained in the entity .
If ` ` role ` ` is provided , only the entity member with the given role are taken into account .""" | if role :
if role . subroles :
role_condition = np . logical_or . reduce ( [ self . members_role == subrole for subrole in role . subroles ] )
else :
role_condition = self . members_role == role
return self . sum ( role_condition )
else :
return np . bincount ( self . members_entity_id ) |
def register_to_payment ( order_class , ** kwargs ) :
"""A function for registering unaware order class to ` ` getpaid ` ` . This will
generate a ` ` Payment ` ` model class that will store payments with
ForeignKey to original order class
This also will build a model class for every enabled backend .""" | global Payment
global Order
class Payment ( PaymentFactory . construct ( order = order_class , ** kwargs ) ) :
objects = PaymentManager ( )
class Meta :
ordering = ( '-created_on' , )
verbose_name = _ ( "Payment" )
verbose_name_plural = _ ( "Payments" )
Order = order_class
# Now build mo... |
def get_type ( self ) :
"""Getting type of measurement keeping backwards compatibility for
v2 API output changes .""" | mtype = None
if "type" not in self . meta_data :
return mtype
mtype = self . meta_data [ "type" ]
if isinstance ( mtype , dict ) :
mtype = self . meta_data . get ( "type" , { } ) . get ( "name" , "" ) . upper ( )
elif isinstance ( mtype , str ) :
mtype = mtype
return mtype |
def is_active ( self ) :
"""Determines whether this plugin is active .
This plugin is only active if TensorBoard sampled any text summaries .
Returns :
Whether this plugin is active .""" | if not self . _multiplexer :
return False
if self . _index_cached is not None : # If we already have computed the index , use it to determine whether
# the plugin should be active , and if so , return immediately .
if any ( self . _index_cached . values ( ) ) :
return True
if self . _multiplexer . Plugi... |
def createCacheRemoveCallback ( cacheRef , key , finalizer ) :
"""Construct a callable to be used as a weakref callback for cache entries .
The callable will invoke the provided finalizer , as well as removing the
cache entry if the cache still exists and contains an entry for the given
key .
@ type cacheRe... | def remove ( reference ) : # Weakref callbacks cannot raise exceptions or DOOM ensues
try :
finalizer ( )
except :
logErrorNoMatterWhat ( )
try :
cache = cacheRef ( )
if cache is not None :
if key in cache . data :
if cache . data [ key ] is refere... |
def describe_api_resource ( restApiId , path , region = None , key = None , keyid = None , profile = None ) :
'''Given rest api id , and an absolute resource path , returns the resource id for
the given path .
CLI Example :
. . code - block : : bash
salt myminion boto _ apigateway . describe _ api _ resourc... | r = describe_api_resources ( restApiId , region = region , key = key , keyid = keyid , profile = profile )
resources = r . get ( 'resources' )
if resources is None :
return r
for resource in resources :
if resource [ 'path' ] == path :
return { 'resource' : resource }
return { 'resource' : None } |
def _backup ( path , filename ) :
"""Backup a file .""" | target = os . path . join ( path , filename )
if os . path . isfile ( target ) :
dt = datetime . now ( )
new_filename = ".{0}.{1}.{2}" . format ( filename , dt . isoformat ( ) , "backup" )
destination = os . path . join ( path , new_filename )
puts ( "- Backing up {0} to {1}" . format ( colored . cyan (... |
def azel2radec ( az_deg : float , el_deg : float , lat_deg : float , lon_deg : float , time : datetime , usevallado : bool = False ) -> Tuple [ float , float ] :
"""viewing angle ( az , el ) to sky coordinates ( ra , dec )
Parameters
az _ deg : float or numpy . ndarray of float
azimuth [ degrees clockwize fro... | if usevallado or Time is None : # non - AstroPy method , less accurate
return vazel2radec ( az_deg , el_deg , lat_deg , lon_deg , time )
obs = EarthLocation ( lat = lat_deg * u . deg , lon = lon_deg * u . deg )
direc = AltAz ( location = obs , obstime = Time ( str2dt ( time ) ) , az = az_deg * u . deg , alt = el_de... |
def act ( self , cmd_name , params = None ) :
"""Run the specified command with its parameters .""" | command = getattr ( self , cmd_name )
if params :
command ( params )
else :
command ( ) |
async def load ( self ) :
"""Load scenes from KLF 200.""" | json_response = await self . pyvlx . interface . api_call ( 'scenes' , 'get' )
self . data_import ( json_response ) |
def remove_links ( text ) :
"""Helper function to remove the links from the input text
Args :
text ( str ) : A string
Returns :
str : the same text , but with any substring that matches the regex
for a link removed and replaced with a space
Example :
> > > from tweet _ parser . getter _ methods . twee... | tco_link_regex = re . compile ( "https?://t.co/[A-z0-9].*" )
generic_link_regex = re . compile ( "(https?://)?(\w*[.]\w+)+([/?=&]+\w+)*" )
remove_tco = re . sub ( tco_link_regex , " " , text )
remove_generic = re . sub ( generic_link_regex , " " , remove_tco )
return remove_generic |
def plot_blob ( sampler , blobidx = 0 , label = None , last_step = False , figure = None , ** kwargs ) :
"""Plot a metadata blob as a fit to spectral data or value distribution
Additional ` ` kwargs ` ` are passed to ` plot _ fit ` .
Parameters
sampler : ` emcee . EnsembleSampler `
Sampler with a stored cha... | modelx , model = _process_blob ( sampler , blobidx , last_step )
if label is None :
label = "Model output {0}" . format ( blobidx )
if modelx is None : # Blob is scalar , plot distribution
f = plot_distribution ( model , label , figure = figure )
else :
f = plot_fit ( sampler , modelidx = blobidx , last_ste... |
def get_presig ( self , target , source , env ) :
"""Return the signature contents of this callable action .""" | try :
return self . gc ( target , source , env )
except AttributeError :
return self . funccontents |
def run_query ( self , collection_name , query ) :
"""method runs query on a specified collection and return a list of filtered Job records""" | cursor = self . ds . filter ( collection_name , query )
return [ Job . from_json ( document ) for document in cursor ] |
def inline ( self ) -> str :
"""Return inline string format of the Membership instance
: return :""" | return "{0}:{1}:{2}:{3}:{4}" . format ( self . issuer , self . signatures [ 0 ] , self . membership_ts , self . identity_ts , self . uid ) |
def CreatePrecisionHelper ( cls , precision ) :
"""Creates a precision helper .
Args :
precision ( str ) : precision of the date and time value , which should
be one of the PRECISION _ VALUES in definitions .
Returns :
class : date time precision helper class .
Raises :
ValueError : if the precision v... | precision_helper_class = cls . _PRECISION_CLASSES . get ( precision , None )
if not precision_helper_class :
raise ValueError ( 'Unsupported precision: {0!s}' . format ( precision ) )
return precision_helper_class |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.