signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
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def md ( cls , data , force_field , temperature , nsteps , other_settings = None ) :
"""Example for a simple MD run based on template md . txt .
Args :
data ( LammpsData or str ) : Data file as a LammpsData
instance or path to an existing data file .
force _ field ( str ) : Combined force field related cmds... | template_path = os . path . join ( cls . template_dir , "md.txt" )
with open ( template_path ) as f :
script_template = f . read ( )
settings = other_settings . copy ( ) if other_settings is not None else { }
settings . update ( { 'force_field' : force_field , "temperature" : temperature , "nsteps" : nsteps } )
scr... |
def parse_path ( root_dir ) :
"""Split path into head and last component for the completer .
Also return position where last component starts .
: param root _ dir : str path
: return : tuple of ( string , string , int )""" | base_dir , last_dir , position = '' , '' , 0
if root_dir :
base_dir , last_dir = os . path . split ( root_dir )
position = - len ( last_dir ) if last_dir else 0
return base_dir , last_dir , position |
def _loadTwoPartSource ( self , sourceFName , sourceLines ) :
"""is a helper for _ loadOneSource .""" | lineno = 1
enterInConfstems = 0
if sourceFName . find ( "conferences" ) != - 1 :
enterInConfstems = 1
for ln in sourceLines :
lineno += 1
try :
stem , source = ln . split ( "\t" , 1 )
stem = stem . strip ( ) [ - 9 : ]
if not source . strip ( ) :
sys . stderr . write ( "so... |
def execute ( filelocation , args , outdir , filters = None , executable = 'msConvert.exe' ) :
"""Execute the msConvert tool on Windows operating systems .
: param filelocation : input file path
: param args : str ( ) or list ( ) , msConvert arguments for details see the
msConvert help below .
: param outdi... | procArgs = [ executable , filelocation ]
procArgs . extend ( aux . toList ( args ) )
if filters is not None :
for arg in aux . toList ( filters ) :
procArgs . extend ( [ '--filter' , arg ] )
procArgs . extend ( [ '-o' , outdir ] )
# # run it # #
proc = subprocess . Popen ( procArgs , stderr = subprocess . P... |
def validate_word_size ( word_size , BLAST_SETS ) :
"""Validate word size in blast / tblastn form .""" | blast_min_int_word_size = BLAST_SETS . min_word_size
blast_max_int_word_size = BLAST_SETS . max_word_size
blast_word_size_error = BLAST_SETS . get_word_size_error ( )
try :
if len ( word_size ) <= 0 :
raise forms . ValidationError ( blast_word_size_error )
int_word_size = int ( word_size )
if int_wo... |
def wirevector_list ( names , bitwidth = None , wvtype = WireVector ) :
"""Allocate and return a list of WireVectors .
: param names : Names for the WireVectors . Can be a list or single comma / space - separated string
: param bitwidth : The desired bitwidth for the resulting WireVectors .
: param WireVector... | if isinstance ( names , str ) :
names = names . replace ( ',' , ' ' ) . split ( )
if any ( '/' in name for name in names ) and bitwidth is not None :
raise PyrtlError ( 'only one of optional "/" or bitwidth parameter allowed' )
if bitwidth is None :
bitwidth = 1
if isinstance ( bitwidth , numbers . Integral... |
def request_frame ( self ) :
"""Construct initiating frame .""" | self . session_id = get_new_session_id ( )
return FrameActivateSceneRequest ( scene_id = self . scene_id , session_id = self . session_id ) |
def pay_dividends ( self , next_trading_day ) :
"""Returns a cash payment based on the dividends that should be paid out
according to the accumulated bookkeeping of earned , unpaid , and stock
dividends .""" | net_cash_payment = 0.0
try :
payments = self . _unpaid_dividends [ next_trading_day ]
# Mark these dividends as paid by dropping them from our unpaid
del self . _unpaid_dividends [ next_trading_day ]
except KeyError :
payments = [ ]
# representing the fact that we ' re required to reimburse the owner of... |
def authenticate_http_request ( token = None ) :
"""Validate auth0 tokens passed in the request ' s header , hence ensuring
that the user is authenticated . Code copied from :
https : / / github . com / auth0 / auth0 - python / tree / master / examples / flask - api
Return a PntCommonException if failed to va... | if token :
auth = token
else :
auth = request . headers . get ( 'Authorization' , None )
if not auth :
auth = request . cookies . get ( 'token' , None )
if auth :
auth = unquote_plus ( auth )
log . debug ( "Validating Auth header [%s]" % auth )
if not auth :
raise AuthMissingHeaderError ( 'T... |
def parse ( text , showToc = True ) :
"""Returns HTML from MediaWiki markup""" | p = Parser ( show_toc = showToc )
return p . parse ( text ) |
def get_hash ( self , handle ) :
"""Get the associated hash for the given handle , the hash file must
exist ( ` ` handle + ' . hash ' ` ` ) .
Args :
handle ( str ) : Path to the template to get the hash from
Returns :
str : Hash for the given handle""" | response = self . open_url ( url = handle , suffix = '.hash' )
try :
return response . read ( )
finally :
response . close ( ) |
def calcparams_pvsyst ( self , effective_irradiance , temp_cell ) :
"""Use the : py : func : ` calcparams _ pvsyst ` function , the input
parameters and ` ` self . module _ parameters ` ` to calculate the
module currents and resistances .
Parameters
effective _ irradiance : numeric
The irradiance ( W / m2... | kwargs = _build_kwargs ( [ 'gamma_ref' , 'mu_gamma' , 'I_L_ref' , 'I_o_ref' , 'R_sh_ref' , 'R_sh_0' , 'R_sh_exp' , 'R_s' , 'alpha_sc' , 'EgRef' , 'irrad_ref' , 'temp_ref' , 'cells_in_series' ] , self . module_parameters )
return calcparams_pvsyst ( effective_irradiance , temp_cell , ** kwargs ) |
def register_name ( self , clsdict ) :
"""Add a member name to the class dict * clsdict * containing the value of
this member object . Where the name of this object is None , do
nothing ; this allows out - of - band values to be defined without adding
a name to the class dict .""" | if self . name is None :
return
clsdict [ self . name ] = self . value |
def workflow_set_visibility ( object_id , input_params = { } , always_retry = True , ** kwargs ) :
"""Invokes the / workflow - xxxx / setVisibility API method .
For more info , see : https : / / wiki . dnanexus . com / API - Specification - v1.0.0 / Visibility # API - method % 3A - % 2Fclass - xxxx % 2FsetVisibil... | return DXHTTPRequest ( '/%s/setVisibility' % object_id , input_params , always_retry = always_retry , ** kwargs ) |
def history ( verbose , range ) :
"""List revision changesets chronologically""" | alembic_command . history ( config = get_config ( ) , rev_range = range , verbose = verbose ) |
def release ( self , conn ) :
"""Returns used connection back into pool .
When returned connection has db index that differs from one in pool
the connection will be closed and dropped .
When queue of free connections is full the connection will be dropped .""" | assert conn in self . _used , ( "Invalid connection, maybe from other pool" , conn )
self . _used . remove ( conn )
if not conn . closed :
if conn . in_transaction :
logger . warning ( "Connection %r is in transaction, closing it." , conn )
conn . close ( )
elif conn . in_pubsub :
logger... |
def all_unambiguous ( sequence_str ) :
"""All unambiguous versions of sequence _ str""" | result = [ [ ] ]
for c in sequence_str :
result = [ i + [ a ] for i in result for a in _AMBIGUOUS_MAP . get ( c , c ) ]
return [ '' . join ( i ) for i in result ] |
def get_logview_address ( self , hours = None ) :
"""Get logview address of the instance object by hours .
: param hours :
: return : logview address
: rtype : str""" | hours = hours or options . log_view_hours
project = self . project
url = '%s/authorization' % project . resource ( )
policy = { 'expires_in_hours' : hours , 'policy' : { 'Statement' : [ { 'Action' : [ 'odps:Read' ] , 'Effect' : 'Allow' , 'Resource' : 'acs:odps:*:projects/%s/instances/%s' % ( project . name , self . id ... |
def p_expression_land ( self , p ) :
'expression : expression LAND expression' | p [ 0 ] = Land ( p [ 1 ] , p [ 3 ] , lineno = p . lineno ( 1 ) )
p . set_lineno ( 0 , p . lineno ( 1 ) ) |
def _do_serialize ( struct , fmt , encoding ) :
"""Actually serialize input .
Args :
struct : structure to serialize to
fmt : format to serialize to
encoding : encoding to use while serializing
Returns :
encoded serialized structure
Raises :
various sorts of errors raised by libraries while serializ... | res = None
_check_lib_installed ( fmt , 'serialize' )
if fmt == 'ini' :
config = configobj . ConfigObj ( encoding = encoding )
for k , v in struct . items ( ) :
config [ k ] = v
res = b'\n' . join ( config . write ( ) )
elif fmt in [ 'json' , 'json5' ] : # specify separators to get rid of trailing w... |
def get_one_parameter ( self , regex_exp , parameters ) :
"""Get three parameters from a given regex expression
Raise an exception if more than three were found
: param regex _ exp :
: param parameters :
: return :""" | Rx , other = self . get_parameters ( regex_exp , parameters )
if other is not None and other . strip ( ) :
raise iarm . exceptions . ParsingError ( "Extra arguments found: {}" . format ( other ) )
return Rx . upper ( ) |
def _create_save_state ( self , link_item_dict : Dict [ str , LinkItem ] ) -> SaveState :
"""Create protobuf savestate of the module and the given data .
: param link _ item _ dict : data
: type link _ item _ dict : Dict [ str , ~ unidown . plugin . link _ item . LinkItem ]
: return : the savestate
: rtype ... | return SaveState ( dynamic_data . SAVE_STATE_VERSION , self . info , self . last_update , link_item_dict ) |
def _run_task_hook ( hooks , method , task , queue_name ) :
"""Invokes hooks . method ( task , queue _ name ) .
Args :
hooks : A hooks . Hooks instance or None .
method : The name of the method to invoke on the hooks class e . g .
" enqueue _ kickoff _ task " .
task : The taskqueue . Task to pass to the h... | if hooks is not None :
try :
getattr ( hooks , method ) ( task , queue_name )
except NotImplementedError : # Use the default task addition implementation .
return False
return True
return False |
def create_user ( self , email , first_name , last_name , password , role = "user" , metadata = { } ) :
"""Create a new user
: type email : str
: param email : User ' s email
: type first _ name : str
: param first _ name : User ' s first name
: type last _ name : str
: param last _ name : User ' s last... | data = { 'firstName' : first_name , 'lastName' : last_name , 'email' : email , 'metadata' : metadata , 'role' : role . upper ( ) if role else role , 'newPassword' : password , }
response = self . post ( 'createUser' , data )
return self . _handle_empty ( email , response ) |
def set_state ( self , state ) :
"""Activate and put this conversation into the given state .
The relation name will be interpolated in the state name , and it is
recommended that it be included to avoid conflicts with states from
other relations . For example : :
conversation . set _ state ( ' { relation _... | state = state . format ( relation_name = self . relation_name )
value = _get_flag_value ( state , { 'relation' : self . relation_name , 'conversations' : [ ] , } )
if self . key not in value [ 'conversations' ] :
value [ 'conversations' ] . append ( self . key )
set_flag ( state , value ) |
def qget ( self , name , index ) :
"""Get the element of ` ` index ` ` within the queue ` ` name ` `
: param string name : the queue name
: param int index : the specified index , can < 0
: return : the value at ` ` index ` ` within queue ` ` name ` ` , or ` ` None ` ` if the
element doesn ' t exist
: rty... | index = get_integer ( 'index' , index )
return self . execute_command ( 'qget' , name , index ) |
async def verify_scriptworker_task ( chain , obj ) :
"""Verify the signing trust object .
Currently the only check is to make sure it was run on a scriptworker .
Args :
chain ( ChainOfTrust ) : the chain we ' re operating on
obj ( ChainOfTrust or LinkOfTrust ) : the trust object for the signing task .""" | errors = [ ]
if obj . worker_impl != "scriptworker" :
errors . append ( "{} {} must be run from scriptworker!" . format ( obj . name , obj . task_id ) )
raise_on_errors ( errors ) |
def usable_id ( cls , id ) :
"""Retrieve id from input which can be ISO , name , country , dc _ code .""" | try : # id is maybe a dc _ code
qry_id = cls . from_dc_code ( id )
if not qry_id : # id is maybe a ISO
qry_id = cls . from_iso ( id )
if qry_id :
cls . deprecated ( 'ISO code for datacenter filter use ' 'dc_code instead' )
if not qry_id : # id is maybe a country
qry_id = ... |
def allpathsX ( args ) :
"""% prog allpathsX folder tag
Run assembly on a folder of paired reads and apply tag ( PE - 200 , PE - 500 ) .
Allow multiple tags separated by comma , e . g . PE - 350 , TT - 1050""" | p = OptionParser ( allpathsX . __doc__ )
opts , args = p . parse_args ( args )
if len ( args ) != 2 :
sys . exit ( not p . print_help ( ) )
folder , tag = args
tag = tag . split ( "," )
for p , pf in iter_project ( folder ) :
assemble_pairs ( p , pf , tag ) |
def _do_functions ( self , rule , p_selectors , p_parents , p_children , scope , media , c_lineno , c_property , c_codestr , code , name ) :
"""Implements @ mixin and @ function""" | if name :
funct , params , _ = name . partition ( '(' )
funct = funct . strip ( )
params = split_params ( depar ( params + _ ) )
defaults = { }
new_params = [ ]
for param in params :
param , _ , default = param . partition ( ':' )
param = param . strip ( )
default = defau... |
def edit_scheme ( self ) :
"""Edit current scheme .""" | dlg = self . scheme_editor_dialog
dlg . set_scheme ( self . current_scheme )
if dlg . exec_ ( ) : # Update temp scheme to reflect instant edits on the preview
temporal_color_scheme = dlg . get_edited_color_scheme ( )
for key in temporal_color_scheme :
option = "temp/{0}" . format ( key )
value =... |
def validate_key_values ( config_handle , section , key , default = None ) :
"""Warn when * key * is missing from configuration * section * .
Args :
config _ handle ( configparser . ConfigParser ) : Instance of configurations .
section ( str ) : Name of configuration section to retrieve .
key ( str ) : Conf... | if section not in config_handle :
LOG . info ( 'Section missing from configurations: [%s]' , section )
try :
value = config_handle [ section ] [ key ]
except KeyError :
LOG . warning ( '[%s] missing key "%s", using %r.' , section , key , default )
value = default
return value |
def predict_from_mutation_effects ( self , effects , transcript_expression_dict = None , gene_expression_dict = None ) :
"""Given a Varcode . EffectCollection of predicted protein effects ,
return predicted epitopes around each mutation .
Parameters
effects : Varcode . EffectCollection
transcript _ expressi... | # we only care about effects which impact the coding sequence of a
# protein
effects = filter_silent_and_noncoding_effects ( effects )
effects = apply_effect_expression_filters ( effects , transcript_expression_dict = transcript_expression_dict , transcript_expression_threshold = self . min_transcript_expression , gene... |
def get_parameter ( self , name ) :
"""Get the parameter on this schema with the given C { name } .""" | for parameter in self . _parameters :
if parameter . name == name :
return parameter |
def get_object ( self , queryset = None ) :
"""Return object with episode number attached to episode .""" | if settings . PODCAST_SINGULAR :
show = get_object_or_404 ( Show , id = settings . PODCAST_ID )
else :
show = get_object_or_404 ( Show , slug = self . kwargs [ 'show_slug' ] )
obj = get_object_or_404 ( Episode , show = show , slug = self . kwargs [ 'slug' ] )
index = Episode . objects . is_public_or_secret ( ) ... |
def get_inputs_helper ( step , ignore , target ) :
"""Recursion helper used by get _ inputs ( )""" | outputs = set ( )
if not ignore and step . target == target :
outputs . add ( step )
if ignore or not step . target :
for i in step . inputs :
outputs . update ( get_inputs_helper ( i , ignore = False , target = target ) )
return outputs |
def get_knob_defaults_as_table ( cls ) :
"""Renders knobs in table
: return :""" | knob_list = [ { 'Knob' : name , 'Description' : cls . get_registered_knob ( name ) . description , 'Default' : cls . get_registered_knob ( name ) . default } for name in sorted ( cls . _register . keys ( ) ) ]
return tabulate . tabulate ( knob_list , headers = 'keys' , tablefmt = 'fancy_grid' ) |
def p_levelsigs ( self , p ) :
'levelsigs : levelsigs SENS _ OR levelsig' | p [ 0 ] = p [ 1 ] + ( p [ 3 ] , )
p . set_lineno ( 0 , p . lineno ( 1 ) ) |
def blend_rect ( self , x0 , y0 , x1 , y1 , dx , dy , destination , alpha = 0xff ) :
"""Blend a rectangle onto the image""" | x0 , y0 , x1 , y1 = self . rect_helper ( x0 , y0 , x1 , y1 )
for x in range ( x0 , x1 + 1 ) :
for y in range ( y0 , y1 + 1 ) :
o = self . _offset ( x , y )
rgba = self . canvas [ o : o + 4 ]
rgba [ 3 ] = alpha
destination . point ( dx + x - x0 , dy + y - y0 , rgba ) |
def business_days ( start , stop ) :
"""Return business days between two inclusive dates - ignoring public holidays .
Note that start must be less than stop or else 0 is returned .
@ param start : Start date
@ param stop : Stop date
@ return int""" | dates = rrule . rruleset ( )
# Get dates between start / stop ( which are inclusive )
dates . rrule ( rrule . rrule ( rrule . DAILY , dtstart = start , until = stop ) )
# Exclude Sat / Sun
dates . exrule ( rrule . rrule ( rrule . DAILY , byweekday = ( rrule . SA , rrule . SU ) , dtstart = start ) )
return dates . count... |
def plot ( self , color = 'default' , ret = False , ax = None ) :
"""Generates a basic 3D visualization .
: param color : Polygons color .
: type color : matplotlib color , ' default ' or ' t ' ( transparent )
: param ret : If True , returns the figure . It can be used to add
more elements to the plot or to... | import matplotlib . pylab as plt
import mpl_toolkits . mplot3d as mplot3d
# Bypass a plot
if color == False :
if ax is None :
ax = mplot3d . Axes3D ( fig = plt . figure ( ) )
return ax
# Clone and extract the information from the object
obj = self . __class__ ( ** self . get_seed ( ) )
plotable3d = obj ... |
def get ( self , remote_file , local_file ) :
"""下载文件
: param remote _ file :
: param local _ file :
: return :""" | sftp = self . get_sftp ( )
try :
sftp . get ( remote_file , local_file )
except Exception as e :
logger . error ( '下载文件失败' )
logger . error ( 'remote: %s, local: %s' % ( remote_file , local_file ) )
logger . error ( e ) |
def _addSpecfile ( self , specfile , path ) :
"""Adds a new specfile entry to SiiContainer . info . See also
: class : ` SiiContainer . addSpecfile ( ) ` .
: param specfile : the name of an ms - run file
: param path : filedirectory for loading and saving the ` ` siic ` ` files""" | self . info [ specfile ] = { 'path' : path , 'qcAttr' : None , 'qcCutoff' : None , 'qcLargerBetter' : None , 'rankAttr' : None , 'rankLargerBetter' : None }
self . container [ specfile ] = dict ( ) |
def readline ( self ) :
"""Readline wrapper to force readline ( ) to return str objects .""" | line = self . fd . __class__ . readline ( self . fd )
if isinstance ( line , bytes ) :
line = line . decode ( )
return line |
def set_value ( self , complete_name , value ) :
"""Set the value for the supplied parameter .""" | element = self . toc . get_element_by_complete_name ( complete_name )
if not element :
logger . warning ( "Cannot set value for [%s], it's not in the TOC!" , complete_name )
raise KeyError ( '{} not in param TOC' . format ( complete_name ) )
elif element . access == ParamTocElement . RO_ACCESS :
logger . de... |
def get_assistants_from_file_hierarchy ( cls , file_hierarchy , superassistant , role = settings . DEFAULT_ASSISTANT_ROLE ) :
"""Accepts file _ hierarch as returned by cls . get _ assistant _ file _ hierarchy and returns
instances of YamlAssistant for loaded files
Args :
file _ hierarchy : structure as descri... | result = [ ]
warn_msg = 'Failed to load assistant {source}, skipping subassistants.'
for name , attrs in file_hierarchy . items ( ) :
loaded_yaml = yaml_loader . YamlLoader . load_yaml_by_path ( attrs [ 'source' ] )
if loaded_yaml is None : # there was an error parsing yaml
logger . warning ( warn_msg .... |
def getblock ( lines ) :
"""Extract the block of code at the top of the given list of lines .""" | try :
tokenize . tokenize ( ListReader ( lines ) . readline , BlockFinder ( ) . tokeneater )
except EndOfBlock , eob :
return lines [ : eob . args [ 0 ] ]
# Fooling the indent / dedent logic implies a one - line definition
return lines [ : 1 ] |
async def end_takeout ( self , success ) :
"""Finishes a takeout , with specified result sent back to Telegram .
Returns :
` ` True ` ` if the operation was successful , ` ` False ` ` otherwise .""" | try :
async with _TakeoutClient ( True , self , None ) as takeout :
takeout . success = success
except ValueError :
return False
return True |
def new ( cls , __name , __fields , ** defaults ) :
'''Creates a new class that can represent a record with the
specified * fields * . This is equal to a mutable namedtuple .
The returned class also supports keyword arguments in its
constructor .
: param _ _ name : The name of the recordclass .
: param _ ... | name = __name
fields = __fields
fieldset = set ( fields )
if isinstance ( fields , str ) :
if ',' in fields :
fields = fields . split ( ',' )
else :
fields = fields . split ( )
else :
fields = list ( fields )
for key in defaults . keys ( ) :
if key not in fields :
fields . append... |
def _addRawResult ( self , resid , values = { } , override = False ) :
"""Structure of values dict ( dict entry for each analysis / field ) :
{ ' ALC ' : { ' ALC ' : ' 13.55 ' ,
' DefaultResult ' : ' ALC ' ,
' Remarks ' : ' ' } ,
' CO2 ' : { ' CO2 ' : ' 0.66 ' ,
' DefaultResult ' : ' CO2 ' ,
' Remarks '... | if 'Date' in values and 'Time' in values :
try :
dtstr = '%s %s' % ( values . get ( 'Date' ) [ 'Date' ] , values . get ( 'Time' ) [ 'Time' ] )
# 2/11/2005 13:33 PM
from datetime import datetime
dtobj = datetime . strptime ( dtstr , '%d/%m/%Y %H:%M %p' )
dateTime = dtobj . str... |
def compute ( self , data , fill_value = None , ** kwargs ) :
"""Resample the given data using bilinear interpolation""" | del kwargs
if fill_value is None :
fill_value = data . attrs . get ( '_FillValue' )
target_shape = self . target_geo_def . shape
res = self . resampler . get_sample_from_bil_info ( data , fill_value = fill_value , output_shape = target_shape )
return res |
def handle_xmlrpc ( self , request_text ) :
"""Handle a single XML - RPC request""" | response = self . _marshaled_dispatch ( request_text )
print ( 'Content-Type: text/xml' )
print ( 'Content-Length: %d' % len ( response ) )
print ( )
sys . stdout . flush ( )
sys . stdout . buffer . write ( response )
sys . stdout . buffer . flush ( ) |
def expectation ( p , obj1 , obj2 = None , nghp = None ) :
"""Compute the expectation < obj1 ( x ) obj2 ( x ) > _ p ( x )
Uses multiple - dispatch to select an analytical implementation ,
if one is available . If not , it falls back to quadrature .
: type p : ( mu , cov ) tuple or a ` ProbabilityDistribution ... | if isinstance ( p , tuple ) :
assert len ( p ) == 2
if p [ 1 ] . shape . ndims == 2 :
p = DiagonalGaussian ( * p )
elif p [ 1 ] . shape . ndims == 3 :
p = Gaussian ( * p )
elif p [ 1 ] . shape . ndims == 4 :
p = MarkovGaussian ( * p )
if isinstance ( obj1 , tuple ) :
obj1 , f... |
def _paload8 ( ins ) :
'''Loads an 8 bit value from a memory address
If 2nd arg . start with ' * ' , it is always treated as
an indirect value .''' | output = _paddr ( ins . quad [ 2 ] )
output . append ( 'ld a, (hl)' )
output . append ( 'push af' )
return output |
def generate_gap_bed ( fname , outname ) :
"""Generate a BED file with gap locations .
Parameters
fname : str
Filename of input FASTA file .
outname : str
Filename of output BED file .""" | f = Fasta ( fname )
with open ( outname , "w" ) as bed :
for chrom in f . keys ( ) :
for m in re . finditer ( r'N+' , f [ chrom ] [ : ] . seq ) :
bed . write ( "{}\t{}\t{}\n" . format ( chrom , m . start ( 0 ) , m . end ( 0 ) ) ) |
def serialize ( self , value , ** kwargs ) :
"""Serialize every item of the list .""" | return [ self . item_type . serialize ( val , ** kwargs ) for val in value ] |
def generate_payload ( self ) :
"""Generate a list of telemetry events as payload""" | events = [ ]
transformation_task = self . _get_alias_transformation_properties ( )
transformation_task . update ( self . _get_based_properties ( ) )
events . append ( transformation_task )
for exception in self . exceptions :
properties = { 'Reserved.DataModel.Fault.TypeString' : exception . __class__ . __name__ , ... |
def generate_component_id_namespace_overview ( model , components ) :
"""Tabulate which MIRIAM databases the component ' s identifier matches .
Parameters
model : cobra . Model
A cobrapy metabolic model .
components : { " metabolites " , " reactions " , " genes " }
A string denoting ` cobra . Model ` comp... | patterns = { "metabolites" : METABOLITE_ANNOTATIONS , "reactions" : REACTION_ANNOTATIONS , "genes" : GENE_PRODUCT_ANNOTATIONS } [ components ]
databases = list ( patterns )
data = list ( )
index = list ( )
for elem in getattr ( model , components ) :
index . append ( elem . id )
data . append ( tuple ( patterns... |
def fft ( xi , yi , axis = 0 ) -> tuple :
"""Take the 1D FFT of an N - dimensional array and return " sensible " properly shifted arrays .
Parameters
xi : numpy . ndarray
1D array over which the points to be FFT ' ed are defined
yi : numpy . ndarray
ND array with values to FFT
axis : int
axis of yi to... | # xi must be 1D
if xi . ndim != 1 :
raise wt_exceptions . DimensionalityError ( 1 , xi . ndim )
# xi must be evenly spaced
spacing = np . diff ( xi )
if not np . allclose ( spacing , spacing . mean ( ) ) :
raise RuntimeError ( "WrightTools.kit.fft: argument xi must be evenly spaced" )
# fft
yi = np . fft . fft ... |
def provStacks ( self , offs , size ) :
'''Returns a stream of provenance stacks at the given offset''' | for _ , iden in self . provseq . slice ( offs , size ) :
stack = self . getProvStack ( iden )
if stack is None :
continue
yield ( iden , stack ) |
def rm_job ( name ) :
'''Remove the specified job from the server .
CLI Example :
. . code - block : : bash
salt chronos - minion - id chronos . rm _ job my - job''' | response = salt . utils . http . query ( "{0}/scheduler/job/{1}" . format ( _base_url ( ) , name ) , method = 'DELETE' , )
return True |
def update ( self , role_sid = values . unset , attributes = values . unset , friendly_name = values . unset ) :
"""Update the UserInstance
: param unicode role _ sid : The SID id of the Role assigned to this user
: param unicode attributes : A valid JSON string that contains application - specific data
: par... | data = values . of ( { 'RoleSid' : role_sid , 'Attributes' : attributes , 'FriendlyName' : friendly_name , } )
payload = self . _version . update ( 'POST' , self . _uri , data = data , )
return UserInstance ( self . _version , payload , service_sid = self . _solution [ 'service_sid' ] , sid = self . _solution [ 'sid' ]... |
def funTransEdgeX ( theta , rho ) :
"""Fringe matrix in X
: param theta : fringe angle , in [ rad ]
: param rho : bend radius , in [ m ]
: return : 2x2 numpy array""" | return np . matrix ( [ [ 1 , 0 ] , [ np . tan ( theta ) / rho , 1 ] ] , dtype = np . double ) |
def create_pod_security_policy ( self , body , ** kwargs ) :
"""create a PodSecurityPolicy
This method makes a synchronous HTTP request by default . To make an
asynchronous HTTP request , please pass async _ req = True
> > > thread = api . create _ pod _ security _ policy ( body , async _ req = True )
> > >... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'async_req' ) :
return self . create_pod_security_policy_with_http_info ( body , ** kwargs )
else :
( data ) = self . create_pod_security_policy_with_http_info ( body , ** kwargs )
return data |
def scan ( self , string ) :
"""Like findall , but also returning matching start and end string locations""" | return list ( self . _scanner_to_matches ( self . pattern . scanner ( string ) , self . run ) ) |
def direct_command_hub ( self , command ) :
"""Send direct hub command""" | self . logger . info ( "direct_command_hub: Command %s" , command )
command_url = ( self . hub_url + '/3?' + command + "=I=3" )
return self . post_direct_command ( command_url ) |
def accuracy ( self , mode : OsuMode ) :
"""Calculated accuracy .
See Also
< https : / / osu . ppy . sh / help / wiki / Accuracy >""" | if mode is OsuMode . osu :
return ( ( 6 * self . count300 + 2 * self . count100 + self . count50 ) / ( 6 * ( self . count300 + self . count100 + self . count50 + self . countmiss ) ) )
if mode is OsuMode . taiko :
return ( ( self . count300 + self . countgeki + ( 0.5 * ( self . count100 + self . countkatu ) ) )... |
def _get_report_string ( time = 'hour' , threshold = 'significant' , online = False ) :
"""Like : func : ` get _ report ` except returns the raw data instead .
: param str time : A string indicating the time range of earthquakes to report . Must be either " hour " ( only earthquakes in the past hour ) , " day " (... | key = _get_report_request ( time , threshold )
result = _get ( key ) if _CONNECTED else _lookup ( key )
if ( _CONNECTED or online ) and _EDITABLE :
_add_to_cache ( key , result )
return result |
def newNodeEatName ( self , name ) :
"""Creation of a new node element . @ ns is optional ( None ) .""" | ret = libxml2mod . xmlNewNodeEatName ( self . _o , name )
if ret is None :
raise treeError ( 'xmlNewNodeEatName() failed' )
__tmp = xmlNode ( _obj = ret )
return __tmp |
def clone ( srcpath , destpath , vcs = None ) :
"""Clone an existing repository .
: param str srcpath : Path to an existing repository
: param str destpath : Desired path of new repository
: param str vcs : Either ` ` git ` ` , ` ` hg ` ` , or ` ` svn ` `
: returns VCSRepo : The newly cloned repository
If... | vcs = vcs or probe ( srcpath )
cls = _get_repo_class ( vcs )
return cls . clone ( srcpath , destpath ) |
def add ( self , conn , key , value , exptime = 0 ) :
"""Store this data , but only if the server * doesn ' t * already
hold data for this key .
: param key : ` ` bytes ` ` , is the key of the item .
: param value : ` ` bytes ` ` , data to store .
: param exptime : ` ` int ` ` is expiration time . If it ' s... | flags = 0
# TODO : fix when exception removed
return ( yield from self . _storage_command ( conn , b'add' , key , value , flags , exptime ) ) |
def normalizeKerningValue ( value ) :
"""Normalizes kerning value .
* * * value * * must be an : ref : ` type - int - float ` .
* Returned value is the same type as input value .""" | if not isinstance ( value , ( int , float ) ) :
raise TypeError ( "Kerning value must be a int or a float, not %s." % type ( value ) . __name__ )
return value |
def status ( self ) :
"""Return string indicating the error encountered on failure .""" | self . _check_valid ( )
if self . _ret_val == swiglpk . GLP_ENOPFS :
return 'No primal feasible solution'
elif self . _ret_val == swiglpk . GLP_ENODFS :
return 'No dual feasible solution'
return str ( swiglpk . glp_get_status ( self . _problem . _p ) ) |
def get_file_path ( dotted_path , extension = 'json' ) :
"""Reads a dotted file path and returns the file path .""" | # If the operating system ' s file path seperator character is in the string
if os . sep in dotted_path or '/' in dotted_path : # Assume the path is a valid file path
return dotted_path
parts = dotted_path . split ( '.' )
if parts [ 0 ] == 'chatterbot' :
parts . pop ( 0 )
parts [ 0 ] = DATA_DIRECTORY
corpus... |
def apply ( self , vpc ) :
"""returns a list of new security groups that will be added""" | assert vpc is not None
# make sure we ' re up to date
self . reload_remote_groups ( )
vpc_groups = self . vpc_groups ( vpc )
self . _apply_groups ( vpc )
# reloads groups from AWS , the authority
self . reload_remote_groups ( )
vpc_groups = self . vpc_groups ( vpc )
groups = { k . name : k for k in vpc_groups }
for x ,... |
def setup_regex ( self ) :
"""Sets up compiled regex objects for parsing the executables from a module .""" | self . _RX_CONTAINS = r"^\s*contains[^\n]*?$"
self . RE_CONTAINS = re . compile ( self . _RX_CONTAINS , re . M | re . I )
# Setup a regex that can extract information about both functions and subroutines
self . _RX_EXEC = r"\n[ \t]*((?P<type>character|real|type|logical|integer|complex)?" + r"(?P<kind>\([a-z0-9_]+\))?)?... |
def _get_seal_key_ntlm2 ( negotiate_flags , exported_session_key , magic_constant ) :
"""3.4.5.3 SEALKEY
Calculates the seal _ key used to seal ( encrypt ) messages . This for authentication where
NTLMSSP _ NEGOTIATE _ EXTENDED _ SESSIONSECURITY has been negotiated . Will weaken the keys
if NTLMSSP _ NEGOTIAT... | if negotiate_flags & NegotiateFlags . NTLMSSP_NEGOTIATE_128 :
seal_key = exported_session_key
elif negotiate_flags & NegotiateFlags . NTLMSSP_NEGOTIATE_56 :
seal_key = exported_session_key [ : 7 ]
else :
seal_key = exported_session_key [ : 5 ]
seal_key = hashlib . md5 ( seal_key + magic_constant ) . digest ... |
def show ( items , command = 'dmenu' , bottom = None , fast = None , case_insensitive = None , lines = None , monitor = None , prompt = None , font = None , background = None , foreground = None , background_selected = None , foreground_selected = None ) :
'''Present a dmenu to the user .
Args :
items ( Iterabl... | # construct args
args = [ command ]
if bottom :
args . append ( '-b' )
if fast :
args . append ( '-f' )
if case_insensitive :
args . append ( '-i' )
if lines is not None :
args . extend ( ( '-l' , str ( lines ) ) )
if monitor is not None :
args . extend ( ( '-m' , str ( monitor ) ) )
if prompt is no... |
def get_enrollment_history_by_regid ( regid , verbose = 'true' , transcriptable_course = 'all' , changed_since_date = '' , include_unfinished_pce_course_reg = False ) :
""": return : a complete chronological list of all the enrollemnts
[ Enrollment ] , where the Enrollment object has a term element .""" | return _json_to_enrollment_list ( _enrollment_search ( regid , verbose , transcriptable_course , changed_since_date ) , include_unfinished_pce_course_reg ) |
async def sinter ( self , keys , * args ) :
"""Return the intersection of sets specified by ` ` keys ` `
Cluster impl :
Querry all keys , intersection and return result""" | k = list_or_args ( keys , args )
res = await self . smembers ( k [ 0 ] )
for arg in k [ 1 : ] :
res &= await self . smembers ( arg )
return res |
def set_filter ( self , text ) :
"""Set regular expression for filter .""" | self . pattern = get_search_regex ( text )
if self . pattern :
self . _parent . setSortingEnabled ( False )
else :
self . _parent . setSortingEnabled ( True )
self . invalidateFilter ( ) |
def log ( self , cause = None , do_message = True , custom_msg = None ) :
"""Loads exception data from the current exception frame - should be called inside the except block
: return :""" | message = error_message ( self , cause = cause )
exc_type , exc_value , exc_traceback = sys . exc_info ( )
traceback_formatted = traceback . format_exc ( )
traceback_val = traceback . extract_tb ( exc_traceback )
md5 = hashlib . md5 ( traceback_formatted . encode ( 'utf-8' ) ) . hexdigest ( )
if md5 in self . _db : # s... |
def _decode ( self , obj , context ) :
"""Initialises a new Python class from a construct using the mapping
passed to the adapter .""" | cls = self . _get_class ( obj . classID )
return cls . from_construct ( obj , context ) |
def basic_types ( self ) :
"""Returns non - postgres types referenced in user supplied model""" | if not self . foreign_key_definitions :
return self . standard_types
else :
tmp = self . standard_types
tmp . append ( 'ForeignKey' )
return tmp |
def create_or_update ( cls , * props , ** kwargs ) :
"""Call to MERGE with parameters map . A new instance will be created and saved if does not already exists ,
this is an atomic operation . If an instance already exists all optional properties specified will be updated .
Note that the post _ create hook isn '... | lazy = kwargs . get ( 'lazy' , False )
relationship = kwargs . get ( 'relationship' )
# build merge query , make sure to update only explicitly specified properties
create_or_update_params = [ ]
for specified , deflated in [ ( p , cls . deflate ( p , skip_empty = True ) ) for p in props ] :
create_or_update_params ... |
def noise_covariance ( fit , dof = 2 , ** kw ) :
"""Covariance taking into account the ' noise covariance ' of the data .
This is technically more realistic for continuously sampled data .
From Faber , 1993""" | ev = fit . eigenvalues
measurement_noise = ev [ - 1 ] / ( fit . n - dof )
return 4 * ev * measurement_noise |
def send_keys ( self , keyserver , * keyids ) :
"""Send keys to a keyserver .""" | result = self . _result_map [ 'list' ] ( self )
log . debug ( 'send_keys: %r' , keyids )
data = _util . _make_binary_stream ( "" , self . _encoding )
args = [ '--keyserver' , keyserver , '--send-keys' ]
args . extend ( keyids )
self . _handle_io ( args , data , result , binary = True )
log . debug ( 'send_keys result: ... |
def stage_tc_create_security_label ( self , label , resource ) :
"""Add a security label to a resource .
Args :
label ( str ) : The security label ( must exit in ThreatConnect ) .
resource ( obj ) : An instance of tcex resource class .""" | sl_resource = resource . security_labels ( label )
sl_resource . http_method = 'POST'
sl_response = sl_resource . request ( )
if sl_response . get ( 'status' ) != 'Success' :
self . log . warning ( '[tcex] Failed adding security label "{}" ({}).' . format ( label , sl_response . get ( 'response' ) . text ) ) |
def _validate_filters_ndb ( cls , filters , model_class ) :
"""Validate ndb . Model filters .""" | if not filters :
return
properties = model_class . _properties
for idx , f in enumerate ( filters ) :
prop , ineq , val = f
if prop not in properties :
raise errors . BadReaderParamsError ( "Property %s is not defined for entity type %s" , prop , model_class . _get_kind ( ) )
# Attempt to cast t... |
def color_check ( color ) :
"""Check input color format .
: param color : input color
: type color : tuple
: return : color as list""" | if isinstance ( color , ( tuple , list ) ) :
if all ( map ( lambda x : isinstance ( x , int ) , color ) ) :
if all ( map ( lambda x : x < 256 , color ) ) :
return list ( color )
if isinstance ( color , str ) :
color_lower = color . lower ( )
if color_lower in TABLE_COLOR . keys ( ) :
... |
def assert_ge ( left , right , message = None , extra = None ) :
"""Raises an AssertionError if left _ hand < right _ hand .""" | assert left >= right , _assert_fail_message ( message , left , right , "<" , extra ) |
def write_secret ( path , ** kwargs ) :
'''Set secret at the path in vault . The vault policy used must allow this .
CLI Example :
. . code - block : : bash
salt ' * ' vault . write _ secret " secret / my / secret " user = " foo " password = " bar "''' | log . debug ( 'Writing vault secrets for %s at %s' , __grains__ [ 'id' ] , path )
data = dict ( [ ( x , y ) for x , y in kwargs . items ( ) if not x . startswith ( '__' ) ] )
try :
url = 'v1/{0}' . format ( path )
response = __utils__ [ 'vault.make_request' ] ( 'POST' , url , json = data )
if response . sta... |
def _make_spec_file ( self ) :
"""Generates the text of an RPM spec file .
Returns :
A list of strings containing the lines of text .""" | # Note that bdist _ rpm can be an old style class .
if issubclass ( BdistRPMCommand , object ) :
spec_file = super ( BdistRPMCommand , self ) . _make_spec_file ( )
else :
spec_file = bdist_rpm . _make_spec_file ( self )
if sys . version_info [ 0 ] < 3 :
python_package = "python"
else :
python_package = ... |
def _init_dict ( self , data , index = None , dtype = None ) :
"""Derive the " _ data " and " index " attributes of a new Series from a
dictionary input .
Parameters
data : dict or dict - like
Data used to populate the new Series
index : Index or index - like , default None
index for the new Series : if... | # Looking for NaN in dict doesn ' t work ( { np . nan : 1 } [ float ( ' nan ' ) ]
# raises KeyError ) , so we iterate the entire dict , and align
if data :
keys , values = zip ( * data . items ( ) )
values = list ( values )
elif index is not None : # fastpath for Series ( data = None ) . Just use broadcasting a... |
def list_nodes_select ( conn = None , call = None ) :
'''Return a list of the VMs that are on the provider , with select fields''' | if not conn :
conn = get_conn ( )
# pylint : disable = E0602
return salt . utils . cloud . list_nodes_select ( list_nodes_full ( conn , 'function' ) , __opts__ [ 'query.selection' ] , call , ) |
def make_serial ( self , data , days , rev = 0 ) :
"""make data in list
if data enough , will return :
[0 ] is the times of high , low or equal
[1 ] is the serial of data .
or return ' ? '
資料數據 list 化 , days 移動平均值
[0 ] 回傳次數
[1 ] 回傳數據""" | raw = data [ : ]
result = [ ]
try :
while len ( raw ) >= days :
result . append ( float ( sum ( raw [ - days : ] ) / days ) )
raw . pop ( )
self . debug_print ( len ( result ) )
result . reverse ( )
re = [ self . cum_serial ( result , rev ) , result ]
return re
except :
retur... |
def example_path ( cls , project , dataset , annotated_dataset , example ) :
"""Return a fully - qualified example string .""" | return google . api_core . path_template . expand ( "projects/{project}/datasets/{dataset}/annotatedDatasets/{annotated_dataset}/examples/{example}" , project = project , dataset = dataset , annotated_dataset = annotated_dataset , example = example , ) |
def send_video ( self , user_id , media_id , title = None , description = None , account = None ) :
"""发送视频消息
详情请参考
http : / / mp . weixin . qq . com / wiki / 7/12a5a320ae96fecdf0e15cb06123de9f . html
: param user _ id : 用户 ID 。 就是你收到的 ` Message ` 的 source
: param media _ id : 发送的视频的媒体ID 。 可以通过 : func : ` u... | video_data = { 'media_id' : media_id , }
if title :
video_data [ 'title' ] = title
if description :
video_data [ 'description' ] = description
data = { 'touser' : user_id , 'msgtype' : 'video' , 'video' : video_data }
return self . _send_custom_message ( data , account = account ) |
def install ( self , dependency ) :
"""Install a new dependency .""" | if not self . pip_installed :
logger . info ( "Need to install a dependency with pip, but no builtin, " "doing it manually (just wait a little, all should go well)" )
self . _brute_force_install_pip ( )
# split to pass several tokens on multiword dependency ( this is very specific for ' - e ' on
# external requ... |
def create_object ( self , text ) :
'''Allow creation of staff members using a full name string .''' | if self . create_field == 'fullName' :
firstName = text . split ( ' ' ) [ 0 ]
lastName = ' ' . join ( text . split ( ' ' ) [ 1 : ] )
return self . get_queryset ( ) . create ( ** { 'firstName' : firstName , 'lastName' : lastName } )
else :
return super ( StaffMemberAutoComplete , self ) . create_object (... |
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