signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def connectExec ( connection , protocol , commandLine ) :
"""Connect a Protocol to a ssh exec session""" | deferred = connectSession ( connection , protocol )
@ deferred . addCallback
def requestSubsystem ( session ) :
return session . requestExec ( commandLine )
return deferred |
def orient ( mag_azimuth , field_dip , or_con ) :
"""uses specified orientation convention to convert user supplied orientations
to laboratory azimuth and plunge""" | or_con = str ( or_con )
if mag_azimuth == - 999 :
return "" , ""
if or_con == "1" : # lab _ mag _ az = mag _ az ; sample _ dip = - dip
return mag_azimuth , - field_dip
if or_con == "2" :
return mag_azimuth - 90. , - field_dip
if or_con == "3" : # lab _ mag _ az = mag _ az ; sample _ dip = 90 . - dip
ret... |
def _Viscosity ( rho , T , fase = None , drho = None ) :
"""Equation for the Viscosity
Parameters
rho : float
Density , [ kg / m3]
T : float
Temperature , [ K ]
fase : dict , optional for calculate critical enhancement
phase properties
drho : float , optional for calculate critical enhancement
[ ∂... | Tr = T / Tc
Dr = rho / rhoc
# Eq 11
H = [ 1.67752 , 2.20462 , 0.6366564 , - 0.241605 ]
mu0 = 100 * Tr ** 0.5 / sum ( [ Hi / Tr ** i for i , Hi in enumerate ( H ) ] )
# Eq 12
I = [ 0 , 1 , 2 , 3 , 0 , 1 , 2 , 3 , 5 , 0 , 1 , 2 , 3 , 4 , 0 , 1 , 0 , 3 , 4 , 3 , 5 ]
J = [ 0 , 0 , 0 , 0 , 1 , 1 , 1 , 1 , 1 , 2 , 2 , 2 , 2 ... |
def _build_http ( http = None ) :
"""Construct an http client suitable for googleapiclient usage w / user agent .""" | if not http :
http = httplib2 . Http ( timeout = HTTP_REQUEST_TIMEOUT , ca_certs = HTTPLIB_CA_BUNDLE )
user_agent = 'Python-httplib2/{} (gzip), {}/{}' . format ( httplib2 . __version__ , 'custodian-gcp' , '0.1' )
return set_user_agent ( http , user_agent ) |
def get_stoplist ( language ) :
"""Returns an built - in stop - list for the language as a set of words .""" | file_path = os . path . join ( "stoplists" , "%s.txt" % language )
try :
stopwords = pkgutil . get_data ( "justext" , file_path )
except IOError :
raise ValueError ( "Stoplist for language '%s' is missing. " "Please use function 'get_stoplists' for complete list of stoplists " "and feel free to contribute by yo... |
def to_unicode ( data , encoding = 'UTF-8' ) :
"""Convert a number of different types of objects to unicode .""" | if isinstance ( data , unicode_type ) :
return data
if isinstance ( data , bytes ) :
return unicode_type ( data , encoding = encoding )
if hasattr ( data , '__iter__' ) :
try :
dict ( data )
except TypeError :
pass
except ValueError : # Assume it ' s a one dimensional data structure
... |
def setxy ( self ) :
"""computes all vertex coordinates ( x , y ) using
an algorithm by Brandes & Kopf .""" | self . _edge_inverter ( )
self . _detect_alignment_conflicts ( )
inf = float ( 'infinity' )
# initialize vertex coordinates attributes :
for l in self . layers :
for v in l :
self . grx [ v ] . root = v
self . grx [ v ] . align = v
self . grx [ v ] . sink = v
self . grx [ v ] . shift... |
def _prepare_forms ( self ) :
"""private function to prepare content for paramType = form""" | content_type = 'application/x-www-form-urlencoded'
if self . __op . consumes and content_type not in self . __op . consumes :
raise errs . SchemaError ( 'content type {0} does not present in {1}' . format ( content_type , self . __op . consumes ) )
return content_type , six . moves . urllib . parse . urlencode ( se... |
def generate ( env ) :
"""Add default tools .""" | for t in SCons . Tool . tool_list ( env [ 'PLATFORM' ] , env ) :
SCons . Tool . Tool ( t ) ( env ) |
def set_syslog_config ( host , username , password , syslog_config , config_value , protocol = None , port = None , firewall = True , reset_service = True , esxi_hosts = None , credstore = None ) :
'''Set the specified syslog configuration parameter . By default , this function will
reset the syslog service after... | ret = { }
# First , enable the syslog firewall ruleset , for each host , if needed .
if firewall and syslog_config == 'loghost' :
if esxi_hosts :
if not isinstance ( esxi_hosts , list ) :
raise CommandExecutionError ( '\'esxi_hosts\' must be a list.' )
for esxi_host in esxi_hosts :
... |
def grab_focus ( self ) :
"""grab window ' s focus . Keyboard and scroll events will be forwarded
to the sprite who has the focus . Check the ' focused ' property of sprite
in the on - render event to decide how to render it ( say , add an outline
when focused = true )""" | scene = self . get_scene ( )
if scene and scene . _focus_sprite != self :
scene . _focus_sprite = self |
def _update_partition_dci_id ( self , tenant_name , dci_id , vrf_prof = None , part_name = None ) :
"""Function to update DCI ID of partition .""" | self . dcnm_obj . update_project ( tenant_name , part_name , dci_id = dci_id , vrf_prof = vrf_prof ) |
def _get_model_cost ( self , formula , model ) :
"""Given a WCNF formula and a model , the method computes the MaxSAT
cost of the model , i . e . the sum of weights of soft clauses that are
unsatisfied by the model .
: param formula : an input MaxSAT formula
: param model : a satisfying assignment
: type ... | model_set = set ( model )
cost = 0
for i , cl in enumerate ( formula . soft ) :
cost += formula . wght [ i ] if all ( l not in model_set for l in filter ( lambda l : abs ( l ) <= self . formula . nv , cl ) ) else 0
return cost |
def fetch_json_by_name ( name ) :
"""Fetch json based on the element name
First gets the href based on a search by name , then makes a
second query to obtain the element json
: method : GET
: param str name : element name
: return : : py : class : ` smc . api . web . SMCResult `""" | result = fetch_meta_by_name ( name )
if result . href :
result = fetch_json_by_href ( result . href )
return result |
def draw ( self ) :
"""Renders the class balance chart on the specified axes from support .""" | # Number of colors is either number of classes or 2
colors = resolve_colors ( len ( self . support_ ) )
if self . _mode == BALANCE :
self . ax . bar ( np . arange ( len ( self . support_ ) ) , self . support_ , color = colors , align = 'center' , width = 0.5 )
# Compare mode
else :
bar_width = 0.35
labels =... |
def concat ( self , * args , ** kwargs ) :
""": type args : FormattedText
: type kwargs : FormattedText""" | for arg in args :
assert self . formatted_text . _is_compatible ( arg ) , "Cannot concat text with different modes"
self . format_args . append ( arg . text )
for kwarg in kwargs :
value = kwargs [ kwarg ]
assert self . formatted_text . _is_compatible ( value ) , "Cannot concat text with different modes... |
def copy_clip_rectangle_list ( self ) :
"""Return the current clip region as a list of rectangles
in user coordinates .
: return :
A list of rectangles ,
as ` ` ( x , y , width , height ) ` ` tuples of floats .
: raises :
: exc : ` CairoError `
if the clip region cannot be represented as a list
of u... | rectangle_list = cairo . cairo_copy_clip_rectangle_list ( self . _pointer )
_check_status ( rectangle_list . status )
rectangles = rectangle_list . rectangles
result = [ ]
for i in range ( rectangle_list . num_rectangles ) :
rect = rectangles [ i ]
result . append ( ( rect . x , rect . y , rect . width , rect .... |
def point_probability ( self , threshold ) :
"""Determine the probability of exceeding a threshold at a grid point based on the ensemble forecasts at
that point .
Args :
threshold : If > = threshold assigns a 1 to member , otherwise 0.
Returns :
EnsembleConsensus""" | point_prob = np . zeros ( self . data . shape [ 1 : ] )
for t in range ( self . data . shape [ 1 ] ) :
point_prob [ t ] = np . where ( self . data [ : , t ] >= threshold , 1.0 , 0.0 ) . mean ( axis = 0 )
return EnsembleConsensus ( point_prob , "point_probability" , self . ensemble_name , self . run_date , self . va... |
def _xray_register_type_fix ( wrapped , instance , args , kwargs ) :
"""Send the actual connection or curser to register type .""" | our_args = list ( copy . copy ( args ) )
if len ( our_args ) == 2 and isinstance ( our_args [ 1 ] , ( XRayTracedConn , XRayTracedCursor ) ) :
our_args [ 1 ] = our_args [ 1 ] . __wrapped__
return wrapped ( * our_args , ** kwargs ) |
def create_estimator ( model_name , hparams , run_config , schedule = "train_and_evaluate" , decode_hparams = None , use_tpu = False , use_tpu_estimator = False , use_xla = False ) :
"""Create a T2T Estimator .""" | model_fn = t2t_model . T2TModel . make_estimator_model_fn ( model_name , hparams , decode_hparams = decode_hparams , use_tpu = use_tpu )
del use_xla
if use_tpu or use_tpu_estimator :
problem = hparams . problem
batch_size = ( problem . tpu_batch_size_per_shard ( hparams ) * run_config . tpu_config . num_shards ... |
def word_freq ( word : str , domain : str = "all" ) -> int :
"""* * Not officially supported . * *
Get word frequency of a word by domain .
This function will make a query to the server of Thai National Corpus .
Internet connection is required .
* * IMPORTANT : * * Currently ( as of 29 April 2019 ) always r... | listdomain = { "all" : "" , "imaginative" : "1" , "natural-pure-science" : "2" , "applied-science" : "3" , "social-science" : "4" , "world-affairs-history" : "5" , "commerce-finance" : "6" , "arts" : "7" , "belief-thought" : "8" , "leisure" : "9" , "others" : "0" , }
url = "http://www.arts.chula.ac.th/~ling/TNCII/corp.... |
def _new_page ( self ) :
"""Helper function to start a new page . Not intended for external use .""" | self . _current_page = Drawing ( * self . _pagesize )
if self . _bgimage :
self . _current_page . add ( self . _bgimage )
self . _pages . append ( self . _current_page )
self . page_count += 1
self . _position = [ 1 , 0 ] |
def _auth ( self , load ) :
'''Authenticate the client , use the sent public key to encrypt the AES key
which was generated at start up .
This method fires an event over the master event manager . The event is
tagged " auth " and returns a dict with information about the auth
event
# Verify that the key w... | if not salt . utils . verify . valid_id ( self . opts , load [ 'id' ] ) :
log . info ( 'Authentication request from invalid id %s' , load [ 'id' ] )
return { 'enc' : 'clear' , 'load' : { 'ret' : False } }
log . info ( 'Authentication request from %s' , load [ 'id' ] )
# 0 is default which should be ' unlimited ... |
def _to_dsn ( hosts ) :
"""Convert a host URI into a dsn for aiopg .
> > > _ to _ dsn ( ' aiopg : / / myhostname : 4242 / mydb ' )
' postgres : / / crate @ myhostname : 4242 / mydb '
> > > _ to _ dsn ( ' aiopg : / / myhostname : 4242 ' )
' postgres : / / crate @ myhostname : 4242 / doc '
> > > _ to _ dsn ... | p = urlparse ( hosts )
try :
user_and_pw , netloc = p . netloc . split ( '@' , maxsplit = 1 )
except ValueError :
netloc = p . netloc
user_and_pw = 'crate'
try :
host , port = netloc . split ( ':' , maxsplit = 1 )
except ValueError :
host = netloc
port = 5432
dbname = p . path [ 1 : ] if p . pat... |
def remove_get_department_uids ( portal ) :
"""Removes getDepartmentUIDs indexes and metadata""" | logger . info ( "Removing filtering by department ..." )
del_index ( portal , "bika_catalog" , "getDepartmentUIDs" )
del_index ( portal , "bika_setup_catalog" , "getDepartmentUID" )
del_index ( portal , CATALOG_ANALYSIS_REQUEST_LISTING , "getDepartmentUIDs" )
del_index ( portal , CATALOG_WORKSHEET_LISTING , "getDepartm... |
def Create ( event_type ) :
"""Factory method creates objects derived from : py : class ` . Event ` with class name matching the : py : class ` . EventType ` .
: param event _ type : number for type of event
: returns : constructed event corresponding to ` ` event _ type ` `
: rtype : : py : class : ` . Event... | if event_type in EventType . Name : # unknown event type gets base class
if EventType . Name [ event_type ] == Event . __name__ :
return Event ( )
else : # instantiate Event subclass with same name as EventType name
return [ t for t in EventFactory . event_list if t . __name__ == EventType . Nam... |
def argmin ( self , rows : List [ Row ] , column : ComparableColumn ) -> List [ Row ] :
"""Takes a list of rows and a column and returns a list containing a single row ( dict from
columns to cells ) that has the minimum numerical value in the given column . We return a list
instead of a single dict to be consis... | if not rows :
return [ ]
value_row_pairs = [ ( row . values [ column . name ] , row ) for row in rows ]
if not value_row_pairs :
return [ ]
# Returns a list containing the row with the max cell value .
return [ sorted ( value_row_pairs , key = lambda x : x [ 0 ] ) [ 0 ] [ 1 ] ] |
def read_and_redirect ( request , notification_id ) :
"""Marks the supplied notification as read and then redirects
to the supplied URL from the ` ` next ` ` URL parameter .
* * IMPORTANT * * : This is CSRF - unsafe method .
Only use it if its okay for you to mark notifications as read without a robust check ... | notification_page = reverse ( 'notifications:all' )
next_page = request . GET . get ( 'next' , notification_page )
if is_safe_url ( next_page ) :
target = next_page
else :
target = notification_page
try :
user_nf = request . user . notifications . get ( pk = notification_id )
if not user_nf . read :
... |
def dump_hex ( ofd , start , len_ , prefix = 0 ) :
"""Convert ` start ` to hex and logs it , 16 bytes per log statement .
https : / / github . com / thom311 / libnl / blob / libnl3_2_25 / lib / msg . c # L760
Positional arguments :
ofd - - function to call with arguments similar to ` logging . debug ` .
sta... | prefix_whitespaces = ' ' * prefix
limit = 16 - ( prefix * 2 )
start_ = start [ : len_ ]
for line in ( start_ [ i : i + limit ] for i in range ( 0 , len ( start_ ) , limit ) ) : # stackoverflow . com / a / 9475354/1198943
hex_lines , ascii_lines = list ( ) , list ( )
for c in line :
hex_lines . append (... |
def mfpt_sensitivity ( T , target , i ) :
r"""Sensitivity matrix of the mean first - passage time from specified state .
Parameters
T : ( M , M ) ndarray
Transition matrix
target : int or list
Target state or set for mfpt computation
i : int
Compute the sensitivity for state ` i `
Returns
S : ( M ... | # check input
T = _types . ensure_ndarray_or_sparse ( T , ndim = 2 , uniform = True , kind = 'numeric' )
target = _types . ensure_int_vector ( target )
# go
if _issparse ( T ) :
_showSparseConversionWarning ( )
mfpt_sensitivity ( T . todense ( ) , target , i )
else :
return dense . sensitivity . mfpt_sensit... |
def setup_continuous_delivery ( self , swap_with_slot , app_type_details , cd_project_url , create_account , vsts_app_auth_token , test , webapp_list ) :
"""Use this method to setup Continuous Delivery of an Azure web site from a source control repository .
: param swap _ with _ slot : the slot to use for deploym... | branch = self . _repo_info . branch or 'refs/heads/master'
self . _validate_cd_project_url ( cd_project_url )
vsts_account_name = self . _get_vsts_account_name ( cd_project_url )
# Verify inputs before we start generating tokens
source_repository , account_name , team_project_name = self . _get_source_repository ( self... |
def selected ( self ) :
"""Check whether all the matched elements are selected .
Returns :
bool""" | query_results = self . map ( lambda el : el . is_selected ( ) , 'selected' ) . results
if query_results :
return all ( query_results )
return False |
def normalize ( location_name , preserve_commas = False ) :
"""Normalize * location _ name * by stripping punctuation and collapsing
runs of whitespace , and return the normalized name .""" | def replace ( match ) :
if preserve_commas and ',' in match . group ( 0 ) :
return ','
return ' '
return NORMALIZATION_RE . sub ( replace , location_name ) . strip ( ) . lower ( ) |
def compete ( source_x , source_o , timeout = None , memlimit = None , cgroup = 'tictactoe' , cgroup_path = '/sys/fs/cgroup' ) :
"""Fights two source files .
Returns either :
* ( ' ok ' , ' x ' | ' draw ' | ' o ' , GAMEPLAY )
* ( ' error ' , GUILTY , REASON , GAMEPLAY )
REASON : = utf8 - encoded error strin... | gameplay = [ ]
for xo , moveresult , log in run_interactive ( source_x , source_o , timeout , memlimit , cgroup , cgroup_path ) :
if moveresult [ 0 ] == 'error' :
return 'error' , xo , moveresult [ 1 ] , gameplay + [ 0 ]
elif moveresult [ 0 ] == 'state_coords' :
gameplay . append ( coords_to_num... |
def cli ( env , ack_all ) :
"""Summary and acknowledgement of upcoming and ongoing maintenance events""" | manager = AccountManager ( env . client )
events = manager . get_upcoming_events ( )
if ack_all :
for event in events :
result = manager . ack_event ( event [ 'id' ] )
event [ 'acknowledgedFlag' ] = result
env . fout ( event_table ( events ) ) |
def set_key ( self , section , key , value ) :
"""Stores given key in settings file .
: param section : Current section to save the key into .
: type section : unicode
: param key : Current key to save .
: type key : unicode
: param value : Current key value to save .
: type value : object""" | LOGGER . debug ( "> Saving '{0}' in '{1}' section with value: '{2}' in settings file." . format ( key , section , foundations . strings . to_string ( value ) ) )
self . __settings . beginGroup ( section )
self . __settings . setValue ( key , QVariant ( value ) )
self . __settings . endGroup ( ) |
def parse_args ( args , kwargs ) :
"""Returns a kwargs dictionary by turning args into kwargs""" | if 'style' in kwargs :
args += ( kwargs [ 'style' ] , )
del kwargs [ 'style' ]
for arg in args :
if not isinstance ( arg , ( bytes , unicode ) ) :
raise ValueError ( "args must be strings:" + repr ( args ) )
if arg . lower ( ) in FG_COLORS :
if 'fg' in kwargs :
raise ValueErr... |
def get_monitor ( self , topics ) :
"""Attempts to find a Monitor in device cloud that matches the provided topics
: param topics : a string list of topics ( e . g . ` ` [ ' DeviceCore [ U ] ' , ' FileDataCore ' ] ) ` ` )
Returns a : class : ` DeviceCloudMonitor ` if found , otherwise None .""" | for monitor in self . get_monitors ( MON_TOPIC_ATTR == "," . join ( topics ) ) :
return monitor
# return the first one , even if there are multiple
return None |
def beta ( self , val : float ) -> None :
"Set beta ( or alpha as makes sense for given optimizer ) ." | if val is None :
return
if 'betas' in self . opt_keys :
self . set_val ( 'betas' , ( self . _mom , listify ( val , self . _beta ) ) )
elif 'alpha' in self . opt_keys :
self . set_val ( 'alpha' , listify ( val , self . _beta ) )
self . _beta = listify ( val , self . _beta ) |
def set_domain_id ( self , value = None , default = False , disable = False ) :
"""Configures the mlag domain - id value
Args :
value ( str ) : The value to configure the domain - id
default ( bool ) : Configures the domain - id using the default keyword
disable ( bool ) : Negates the domain - id using the ... | return self . _configure_mlag ( 'domain-id' , value , default , disable ) |
def msgHasAcceptableInstId ( self , msg , frm ) -> bool :
"""Return true if the instance id of message corresponds to a correct
replica .
: param msg : the node message to validate
: return :""" | # TODO : refactor this ! this should not do anything except checking !
instId = getattr ( msg , f . INST_ID . nm , None )
if not ( isinstance ( instId , int ) and instId >= 0 ) :
return False
if instId >= self . requiredNumberOfInstances :
if instId not in self . msgsForFutureReplicas :
self . msgsForFu... |
def angle ( self ) :
"""Angle value .""" | if self . use_global_light :
return self . _image_resources . get_data ( 'global_angle' , 30.0 )
return self . value . get ( Key . LocalLightingAngle ) . value |
def _prepare_output ( partitions , verbose ) :
"""Returns dict with ' raw ' and ' message ' keys filled .""" | out = { }
partitions_count = len ( partitions )
out [ 'raw' ] = { 'offline_count' : partitions_count , }
if partitions_count == 0 :
out [ 'message' ] = 'No offline partitions.'
else :
out [ 'message' ] = "{count} offline partitions." . format ( count = partitions_count )
if verbose :
lines = ( '{}:{... |
def setShowGridRows ( self , state ) :
"""Sets whether or not the grid rows should be rendered when drawing the \
grid .
: param state | < bool >""" | delegate = self . itemDelegate ( )
if ( isinstance ( delegate , XTreeWidgetDelegate ) ) :
delegate . setShowGridRows ( state ) |
def _calc_T_var ( self , X ) -> int :
"""Calculate the number of samples , T , from the shape of X""" | shape = X . shape
tensor_rank : int = len ( shape )
if tensor_rank == 0 :
return 1
if tensor_rank == 1 :
return shape [ 0 ]
if tensor_rank == 2 :
if shape [ 1 ] > 1 :
raise ValueError ( 'Initial value of a variable must have dimension T*1.' )
return shape [ 0 ] |
def _inline ( ins ) :
"""Inline code""" | tmp = [ x . strip ( ' \t\r\n' ) for x in ins . quad [ 1 ] . split ( '\n' ) ]
# Split lines
i = 0
while i < len ( tmp ) :
if not tmp [ i ] or tmp [ i ] [ 0 ] == ';' : # a comment or empty string ?
tmp . pop ( i )
continue
if tmp [ i ] [ 0 ] == '#' : # A preprocessor directive
i += 1
... |
def safe_url ( self , url , errors = 'strict' ) :
"""URL encode value for safe HTTP request .
Args :
url ( string ) : The string to URL Encode .
Returns :
( string ) : The urlencoded string .""" | if url is not None :
url = quote ( self . s ( url , errors = errors ) , safe = '~' )
return url |
def get_bandstructure_by_material_id ( self , material_id , line_mode = True ) :
"""Get a BandStructure corresponding to a material _ id .
REST Endpoint : https : / / www . materialsproject . org / rest / v2 / materials / < mp - id > / vasp / bandstructure or
https : / / www . materialsproject . org / rest / v2... | prop = "bandstructure" if line_mode else "bandstructure_uniform"
data = self . get_data ( material_id , prop = prop )
return data [ 0 ] [ prop ] |
def get_gam_splines ( start = 0 , end = 100 , n_bases = 10 , spline_order = 3 , add_intercept = True ) :
"""Main function required by ( TF ) Concise class""" | # make sure n _ bases is an int
assert type ( n_bases ) == int
x = np . arange ( start , end + 1 )
knots = get_knots ( start , end , n_bases , spline_order )
X_splines = get_X_spline ( x , knots , n_bases , spline_order , add_intercept )
S = get_S ( n_bases , spline_order , add_intercept )
# Get the same knot positions... |
def my_init ( self ) :
"""Method automatically called from base class constructor .""" | self . _start_time = time . time ( )
self . _stats = { }
self . _stats_lock = threading . Lock ( ) |
def reverse_complement ( self ) :
'''str : Returns the reverse complement of ` ` Sequence . sequence ` ` .''' | if self . _reverse_complement is None :
self . _reverse_complement = self . _get_reverse_complement ( )
return self . _reverse_complement |
def get_tensor_info ( self ) :
"""See base class for details .""" | return { feature_key : feature . get_tensor_info ( ) for feature_key , feature in self . _feature_dict . items ( ) } |
def _SanitizeField ( self , field ) :
"""Sanitizes a field for output .
This method replaces any field delimiters with a space .
Args :
field ( str ) : name of the field to sanitize .
Returns :
str : value of the field .""" | if self . _field_delimiter and isinstance ( field , py2to3 . STRING_TYPES ) :
return field . replace ( self . _field_delimiter , ' ' )
return field |
def run_parallel ( pipeline , input_gen , options = { } , ncpu = 4 , chunksize = 200 ) :
"""Run a pipeline in parallel over a input generator cutting it into small
chunks .
> > > # if we have a simple component
> > > from reliure . pipeline import Composable
> > > # that we want to run over a given input : ... | t0 = time ( )
# FIXME : there is a know issue when pipeline results are " big " object , the merge is bloking . . . to be investigate
# TODO : add get _ pipeline args to prodvide a fct to build the pipeline ( in each worker )
logger = logging . getLogger ( "reliure.run_parallel" )
jobs = [ ]
results = [ ]
Qdata = mp . ... |
def cancel ( self , mark_completed_as_cancelled = False ) :
"""Cancel the future . If the future has not been started yet , it will never
start running . If the future is already running , it will run until the
worker function exists . The worker function can check if the future has
been cancelled using the :... | with self . _lock :
if not self . _completed or mark_completed_as_cancelled :
self . _cancelled = True
callbacks = self . _prepare_done_callbacks ( )
callbacks ( ) |
def has_mixed_eol_chars ( text ) :
"""Detect if text has mixed EOL characters""" | eol_chars = get_eol_chars ( text )
if eol_chars is None :
return False
correct_text = eol_chars . join ( ( text + eol_chars ) . splitlines ( ) )
return repr ( correct_text ) != repr ( text ) |
def conv_from_name ( name ) :
"""Understand simulink syntax for fixed types and returns the proper
conversion structure .
@ param name : the type name as in simulin ( i . e . UFix _ 8_7 . . . )
@ raise ConversionError : When cannot decode the string""" | _match = re . match ( r"^(?P<signed>u?fix)_(?P<bits>\d+)_(?P<binary>\d+)" , name , flags = re . I )
if not _match :
raise ConversionError ( "Cannot interpret name: " + name )
params = _match . groupdict ( )
if params [ 'signed' ] == 'fix' :
signed = True
else :
signed = False
bits = int ( params [ 'bits' ] ... |
def _check_status ( self ) :
"""Check repo status and except if dirty .""" | logger . info ( 'Checking repo status' )
status = self . log_call ( [ 'git' , 'status' , '--porcelain' ] , callwith = subprocess . check_output , cwd = self . cwd , )
if status :
raise DirtyException ( status ) |
def bilinear_interp ( data , x , y ) :
"""Interpolate input ` ` data ` ` at " pixel " coordinates ` ` x ` ` and ` ` y ` ` .""" | x = np . asarray ( x )
y = np . asarray ( y )
if x . shape != y . shape :
raise ValueError ( "X- and Y-coordinates must have identical shapes." )
out_shape = x . shape
out_size = x . size
x = x . ravel ( )
y = y . ravel ( )
x0 = np . empty ( out_size , dtype = np . int )
y0 = np . empty ( out_size , dtype = np . in... |
def changelist_view ( self , request , extra_context = None ) :
"""Get object currently tracked and add a button to get back to it""" | extra_context = extra_context or { }
if 'object' in request . GET . keys ( ) :
value = request . GET [ 'object' ] . split ( ':' )
content_type = get_object_or_404 ( ContentType , id = value [ 0 ] , )
tracked_object = get_object_or_404 ( content_type . model_class ( ) , id = value [ 1 ] , )
extra_context... |
def show ( self , ticket ) :
"""通过ticket换取二维码
详情请参考
https : / / mp . weixin . qq . com / wiki ? t = resource / res _ main & id = mp1443433542
: param ticket : 二维码 ticket 。 可以通过 : func : ` create ` 获取到
: return : 返回的 Request 对象
使用示例 : :
from wechatpy import WeChatClient
client = WeChatClient ( ' appid ... | if isinstance ( ticket , dict ) :
ticket = ticket [ 'ticket' ]
return requests . get ( url = 'https://mp.weixin.qq.com/cgi-bin/showqrcode' , params = { 'ticket' : ticket } ) |
def resolve_url ( self , resource_name ) :
"""Return a URL to a local copy of a resource , suitable for get _ generator ( )""" | if self . target_format == 'csv' and self . target_file != DEFAULT_METATAB_FILE : # For CSV packages , need to get the package and open it to get the resoruce URL , becuase
# they are always absolute web URLs and may not be related to the location of the metadata .
s = self . get_resource ( )
rs = s . doc . res... |
def normalize_reference_name ( name ) :
"""Search the dictionary of species - specific references to find a reference
name that matches aside from capitalization .
If no matching reference is found , raise an exception .""" | lower_name = name . strip ( ) . lower ( )
for reference in Species . _reference_names_to_species . keys ( ) :
if reference . lower ( ) == lower_name :
return reference
raise ValueError ( "Reference genome '%s' not found" % name ) |
def main ( ) :
"""Main entry point for iotile - sgcompile .""" | arg_parser = build_args ( )
args = arg_parser . parse_args ( )
model = DeviceModel ( )
parser = SensorGraphFileParser ( )
parser . parse_file ( args . sensor_graph )
if args . format == u'ast' :
write_output ( parser . dump_tree ( ) , True , args . output )
sys . exit ( 0 )
parser . compile ( model )
if not arg... |
def create_pipeline ( self , name , description , ** kwargs ) :
'''Creates a pipeline with the provided attributes .
Args :
namerequired name string
kwargs { name , description , orgWide , aclEntries } user
specifiable ones only
return ( status code , pipeline _ dict ) ( as created )''' | # req sanity check
if not ( name and description ) :
return requests . codes . bad_request , None
kwargs . update ( { 'name' : name , 'description' : description } )
new_pl = StreakPipeline ( ** kwargs )
uri = '/' . join ( [ self . api_uri , self . pipelines_suffix ] )
code , r_data = self . _req ( 'put' , uri , ne... |
def inject_experiment ( ) :
"""Inject experiment and enviroment variables into the template context .""" | exp = Experiment ( session )
return dict ( experiment = exp , env = os . environ ) |
def session_rollback ( self , session ) :
"""Send session _ rollback signal in sqlalchemy ` ` after _ rollback ` ` .
This marks the failure of session so the session may enter commit
phase .""" | # this may happen when there ' s nothing to rollback
if not hasattr ( session , 'meepo_unique_id' ) :
self . logger . debug ( "skipped - session_rollback" )
return
# del session meepo id after rollback
self . logger . debug ( "%s - after_rollback" % session . meepo_unique_id )
signal ( "session_rollback" ) . se... |
def geostrophic_wind ( heights , f , dx , dy ) :
r"""Calculate the geostrophic wind given from the heights or geopotential .
Parameters
heights : ( M , N ) ndarray
The height field , with either leading dimensions of ( x , y ) or trailing dimensions
of ( y , x ) , depending on the value of ` ` dim _ order `... | if heights . dimensionality [ '[length]' ] == 2.0 :
norm_factor = 1. / f
else :
norm_factor = mpconsts . g / f
dhdy = first_derivative ( heights , delta = dy , axis = - 2 )
dhdx = first_derivative ( heights , delta = dx , axis = - 1 )
return - norm_factor * dhdy , norm_factor * dhdx |
def _interpolate ( im , x , y , name ) :
"""Perform bilinear sampling on im given x , y coordiantes .
Implements the differentiable sampling mechanism with bilinear kerenl
in https : / / arxiv . org / abs / 1506.02025.
Modified from https : / / github . com / tensorflow / models / tree / master / transformer ... | with tf . variable_scope ( name ) :
x = tf . reshape ( x , [ - 1 ] )
y = tf . reshape ( y , [ - 1 ] )
# constants
num_batch = tf . shape ( im ) [ 0 ]
_ , height , width , channels = im . get_shape ( ) . as_list ( )
x = tf . to_float ( x )
y = tf . to_float ( y )
height_f = tf . cast ( he... |
def build_tree ( X , y , criterion , max_depth , current_depth = 1 ) :
"""Builds the decision tree .""" | # check for max _ depth accomplished
if max_depth >= 0 and current_depth >= max_depth :
return Leaf ( y )
# check for 0 gain
gain , question = find_best_question ( X , y , criterion )
if gain == 0 :
return Leaf ( y )
# split
true_X , false_X , true_y , false_y = split ( X , y , question )
# Build the ` true ` b... |
def print ( root ) : # type : ( Union [ Nonterminal , Terminal , Rule ] ) - > str
"""Transform the parsed tree to the string . Expects tree like structure .
You can see example output below .
( R ) SplitRules26
| - - ( N ) Iterate
| ` - - ( R ) SplitRules30
| ` - - ( N ) Symb
| ` - - ( R ) SplitRules4
... | # print the part before the element
def print_before ( previous = 0 , defined = None , is_last = False ) :
defined = defined or { }
ret = ''
if previous != 0 :
for i in range ( previous - 1 ) : # if the column is still active write |
if i in defined :
ret += '| '
... |
def _add_inline_definition ( item , statement ) :
'''Adds an inline definition to statement .''' | global _current_statement
backup = _current_statement
type_ , options = _expand_one_key_dictionary ( item )
_current_statement = UnnamedStatement ( type = type_ )
_parse_statement ( options )
statement . add_child ( _current_statement )
_current_statement = backup |
def center_cell_text ( cell ) :
"""Horizontally center the text within a cell ' s grid
Like this : :
| foo | - - > | foo |
Parameters
cell : dashtable . data2rst . Cell
Returns
cell : dashtable . data2rst . Cell""" | lines = cell . text . split ( '\n' )
cell_width = len ( lines [ 0 ] ) - 2
truncated_lines = [ '' ]
for i in range ( 1 , len ( lines ) - 1 ) :
truncated = lines [ i ] [ 2 : len ( lines [ i ] ) - 2 ] . rstrip ( )
truncated_lines . append ( truncated )
truncated_lines . append ( '' )
max_line_length = get_longest_... |
def output ( data , ** kwargs ) : # pylint : disable = unused - argument
'''Print out via pretty print''' | if isinstance ( data , Exception ) :
data = six . text_type ( data )
if 'output_indent' in __opts__ and __opts__ [ 'output_indent' ] >= 0 :
return pprint . pformat ( data , indent = __opts__ [ 'output_indent' ] )
return pprint . pformat ( data ) |
def count_de_novos_per_transcript ( ensembl , gene_id , de_novos = [ ] ) :
"""count de novos in transcripts for a gene .
Args :
ensembl : EnsemblRequest object to request data from ensembl
gene _ id : HGNC symbol for gene
de _ novos : list of de novo positions , so we can check they all fit in
the gene tr... | transcripts = get_transcript_ids ( ensembl , gene_id )
# TODO : allow for genes without any coding sequence .
if len ( transcripts ) == 0 :
raise IndexError ( "{0} lacks coding transcripts" . format ( gene_id ) )
# count the de novos observed in all transcripts
counts = { }
for key in transcripts :
try :
... |
def get_account ( self , account , use_sis_id = False , ** kwargs ) :
"""Retrieve information on an individual account .
: calls : ` GET / api / v1 / accounts / : id < https : / / canvas . instructure . com / doc / api / accounts . html # method . accounts . show > ` _
: param account : The object or ID of the ... | if use_sis_id :
account_id = account
uri_str = 'accounts/sis_account_id:{}'
else :
account_id = obj_or_id ( account , "account" , ( Account , ) )
uri_str = 'accounts/{}'
response = self . __requester . request ( 'GET' , uri_str . format ( account_id ) , _kwargs = combine_kwargs ( ** kwargs ) )
return Ac... |
def _get_leftMargin ( self ) :
"""This must return an int or float .
If the glyph has no outlines , this must return ` None ` .
Subclasses may override this method .""" | bounds = self . bounds
if bounds is None :
return None
xMin , yMin , xMax , yMax = bounds
return xMin |
def parse_comparison_operation ( operation : str ) -> Tuple [ Optional [ str ] , str ] :
"""Parse the comparision operator in an operation .""" | _operation = operation . strip ( )
if not _operation :
raise QueryParserException ( 'Operation is not valid: {}' . format ( operation ) )
# Check inclusion comparison
if _operation [ : 2 ] in ( '<=' , '=<' ) :
return '<=' , _operation [ 2 : ] . strip ( )
if _operation [ : 2 ] in ( '>=' , '=>' ) :
return '>=... |
def _ordered_categories ( df , categories ) :
"""Make the columns in df categorical
Parameters :
categories : dict
Of the form { str : list } ,
where the key the column name and the value is
the ordered category list""" | for col , cats in categories . items ( ) :
df [ col ] = df [ col ] . astype ( CategoricalDtype ( cats , ordered = True ) )
return df |
def _filter_parameters ( parameters ) :
"""Filters the ignored parameters out .""" | if not parameters :
return None
return OrderedDict ( ( param , value ) for param , value in six . iteritems ( parameters ) if param not in IGNORED_PARAMS ) |
def is_en_passant ( self , move : Move ) -> bool :
"""Checks if the given pseudo - legal move is an en passant capture .""" | return ( self . ep_square == move . to_square and bool ( self . pawns & BB_SQUARES [ move . from_square ] ) and abs ( move . to_square - move . from_square ) in [ 7 , 9 ] and not self . occupied & BB_SQUARES [ move . to_square ] ) |
def ref ( self ) :
"""Get the reference number of the dataset .
Args : :
no argument
Returns : :
dataset reference number
C library equivalent : SDidtoref""" | sds_ref = _C . SDidtoref ( self . _id )
_checkErr ( 'idtoref' , sds_ref , 'illegal SDS identifier' )
return sds_ref |
def calculateProbableRootOfGeneTree ( speciesTree , geneTree , processID = lambda x : x ) :
"""Goes through each root possible branch making it the root .
Returns tree that requires the minimum number of duplications .""" | # get all rooted trees
# run dup calc on each tree
# return tree with fewest number of dups
if geneTree . traversalID . midEnd <= 3 :
return ( 0 , 0 , geneTree )
checkGeneTreeMatchesSpeciesTree ( speciesTree , geneTree , processID )
l = [ ]
def fn ( tree ) :
if tree . traversalID . mid != geneTree . left . trav... |
def tune ( runner , kernel_options , device_options , tuning_options ) :
"""Find the best performing kernel configuration in the parameter space
: params runner : A runner from kernel _ tuner . runners
: type runner : kernel _ tuner . runner
: param kernel _ options : A dictionary with all options for the ker... | results = [ ]
cache = { }
# scale variables in x because PSO works with velocities to visit different configurations
tuning_options [ "scaling" ] = True
# using this instead of get _ bounds because scaling is used
bounds , _ , _ = get_bounds_x0_eps ( tuning_options )
args = ( kernel_options , tuning_options , runner , ... |
def LearnToExecute ( # pylint : disable = invalid - name
batch_size , max_length = 1 , max_nesting = 1 , token_by_char = True , mode = Mode . TRAIN_COMBINE , loss_threshold = 0.1 , min_tries = DEFAULT_MIN_CURRICULUM_EVAL_TRIES , task_type = TaskType . ALG_CTRL ) :
"""Factory method for LearnToExecute Dataset module... | # defaults mode to " train - combine "
if mode == Mode . TRAIN_COMBINE :
curriculum = CombineCurriculum ( max_length , max_nesting , loss_threshold , min_tries = min_tries )
elif mode == Mode . TRAIN_MIX :
curriculum = MixCurriculum ( max_length , max_nesting , loss_threshold , min_tries = min_tries )
elif mode... |
def apparent_temp ( temp , rh , wind ) :
"""Compute apparent temperature ( real feel ) , using formula from
http : / / www . bom . gov . au / info / thermal _ stress /""" | if temp is None or rh is None or wind is None :
return None
vap_press = ( float ( rh ) / 100.0 ) * 6.105 * math . exp ( 17.27 * temp / ( 237.7 + temp ) )
return temp + ( 0.33 * vap_press ) - ( 0.70 * wind ) - 4.00 |
def find_srv_by_name_and_hostname ( self , host_name , sdescr ) :
"""Get a specific service based on a host _ name and service _ description
: param host _ name : host name linked to needed service
: type host _ name : str
: param sdescr : service name we need
: type sdescr : str
: return : the service fo... | key = ( host_name , sdescr )
return self . name_to_item . get ( key , None ) |
def _update_status ( self , sub_job_num = None ) :
"""Gets the job status .
Return :
str : The current status of the job""" | job_id = '%s.%s' % ( self . cluster_id , sub_job_num ) if sub_job_num else str ( self . cluster_id )
format = [ '-format' , '"%d"' , 'JobStatus' ]
cmd = 'condor_q {0} {1} && condor_history {0} {1}' . format ( job_id , ' ' . join ( format ) )
args = [ cmd ]
out , err = self . _execute ( args , shell = True , run_in_job_... |
def config_string ( self ) :
"""See the class documentation .""" | # Note : _ write _ to _ conf is determined when the value is calculated . This
# is a hidden function call due to property magic .
val = self . str_value
if not self . _write_to_conf :
return ""
if self . orig_type in _BOOL_TRISTATE :
return "{}{}={}\n" . format ( self . kconfig . config_prefix , self . name , ... |
def create_hook ( self , name , config , events = github . GithubObject . NotSet , active = github . GithubObject . NotSet ) :
""": calls : ` POST / orgs / : owner / hooks < http : / / developer . github . com / v3 / orgs / hooks > ` _
: param name : string
: param config : dict
: param events : list of strin... | assert isinstance ( name , ( str , unicode ) ) , name
assert isinstance ( config , dict ) , config
assert events is github . GithubObject . NotSet or all ( isinstance ( element , ( str , unicode ) ) for element in events ) , events
assert active is github . GithubObject . NotSet or isinstance ( active , bool ) , active... |
def getVariantAnnotations ( self , referenceName , startPosition , endPosition ) :
"""Generator for iterating through variant annotations in this
variant annotation set .
: param referenceName :
: param startPosition :
: param endPosition :
: return : generator of protocol . VariantAnnotation""" | variantIter = self . _variantSet . getPysamVariants ( referenceName , startPosition , endPosition )
for record in variantIter :
yield self . convertVariantAnnotation ( record ) |
def _get_usage ( self , account_number , number ) :
"""Get Fido usage .
Get the following data
- talk
- text
- data
Roaming data is not supported yet""" | # Prepare data
data = { "ctn" : number , "language" : "en-US" , "accountNumber" : account_number }
# Http request
try :
raw_res = yield from self . _session . post ( USAGE_URL , data = data , headers = self . _headers , timeout = self . _timeout )
except OSError :
raise PyFidoError ( "Can not get usage" )
# Loa... |
def sort_timeseries ( self , ascending = True ) :
"""Sorts the data points within the TimeSeries according to their occurrence inline .
: param boolean ascending : Determines if the TimeSeries will be ordered ascending or
descending . If this is set to descending once , the ordered parameter defined in
: py :... | # the time series is sorted by default
if ascending and self . _sorted :
return
sortorder = 1
if not ascending :
sortorder = - 1
self . _predefinedSorted = False
self . _timeseriesData . sort ( key = lambda i : sortorder * i [ 0 ] )
self . _sorted = ascending
return self |
def params ( self ) :
"""Returns a list where each element is a nicely formatted
parameter of this function . This includes argument lists ,
keyword arguments and default values .""" | def fmt_param ( el ) :
if isinstance ( el , str ) or isinstance ( el , unicode ) :
return el
else :
return '(%s)' % ( ', ' . join ( map ( fmt_param , el ) ) )
try :
getspec = getattr ( inspect , 'getfullargspec' , inspect . getargspec )
s = getspec ( self . func )
except TypeError : # I ... |
def generate_PVdelV_nt_pos_vecs ( self , generative_model , genomic_data ) :
"""Process P ( delV | V ) into Pi arrays .
Set the attributes PVdelV _ nt _ pos _ vec and PVdelV _ 2nd _ nt _ pos _ per _ aa _ vec .
Parameters
generative _ model : GenerativeModelVJ
VJ generative model class containing the model p... | cutV_genomic_CDR3_segs = genomic_data . cutV_genomic_CDR3_segs
nt2num = { 'A' : 0 , 'C' : 1 , 'G' : 2 , 'T' : 3 }
num_del_pos = generative_model . PdelV_given_V . shape [ 0 ]
num_V_genes = generative_model . PdelV_given_V . shape [ 1 ]
PVdelV_nt_pos_vec = [ [ ] ] * num_V_genes
PVdelV_2nd_nt_pos_per_aa_vec = [ [ ] ] * n... |
def add_material ( self , material ) :
"""Add a material to the mesh , IF it ' s not already present .""" | if self . has_material ( material ) :
return
self . materials . append ( material ) |
def acquaint_insides ( swap_gate : ops . Gate , acquaintance_gate : ops . Operation , qubits : Sequence [ ops . Qid ] , before : bool , layers : Layers , mapping : Dict [ ops . Qid , int ] ) -> None :
"""Acquaints each of the qubits with another set specified by an
acquaintance gate .
Args :
qubits : The list... | max_reach = _get_max_reach ( len ( qubits ) , round_up = before )
reaches = itertools . chain ( range ( 1 , max_reach + 1 ) , range ( max_reach , - 1 , - 1 ) )
offsets = ( 0 , 1 ) * max_reach
swap_gate = SwapPermutationGate ( swap_gate )
ops = [ ]
for offset , reach in zip ( offsets , reaches ) :
if offset == befor... |
def get_att_mats ( translate_model ) :
"""Get ' s the tensors representing the attentions from a build model .
The attentions are stored in a dict on the Transformer object while building
the graph .
Args :
translate _ model : Transformer object to fetch the attention weights from .
Returns :
Tuple of a... | enc_atts = [ ]
dec_atts = [ ]
encdec_atts = [ ]
prefix = "transformer/body/"
postfix_self_attention = "/multihead_attention/dot_product_attention"
if translate_model . hparams . self_attention_type == "dot_product_relative" :
postfix_self_attention = ( "/multihead_attention/" "dot_product_attention_relative" )
post... |
def setConf ( self , conf , type = 'simu' ) :
"""set information for different type dict ,
: param conf : configuration information , str or dict
: param type : simu , ctrl , misc""" | if conf is None :
return
else :
if isinstance ( conf , str ) :
conf = MagBlock . str2dict ( conf )
self . setConfDict [ type ] ( conf ) |
def updateQueue ( destinationRoot , queueDict , debug = False ) :
"""With a dictionary that represents a queue entry , update the queue entry with
the values""" | attrDict = bagatom . AttrDict ( queueDict )
url = urlparse . urljoin ( destinationRoot , "APP/queue/" + attrDict . ark + "/" )
queueXML = bagatom . queueEntryToXML ( attrDict )
urlID = os . path . join ( destinationRoot , attrDict . ark )
uploadXML = bagatom . wrapAtom ( queueXML , id = urlID , title = attrDict . ark )... |
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