signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def gaussian1 ( height , x0 , y0 , a , b , c ) :
"""height - the amplitude of the gaussian
x0 , y0 , - center of the gaussian
a , b , c - ellipse parameters ( coefficients in the quadratic form )""" | return lambda x , y : height * np . exp ( - 0.5 * ( a * ( x - x0 ) ** 2 + b * ( x - x0 ) * ( y - y0 ) + c * ( y - y0 ) ** 2 ) ) |
def write_file ( writer , filename ) :
"""Write all of lines from file using the writer .""" | for line in txt_line_iterator ( filename ) :
writer . write ( line )
writer . write ( "\n" ) |
def get_thumbnail_image_url ( self , page = 1 ) :
"""Returns the URL for the thumbnail sized image of a single page .
The page kwarg specifies which page to return . One is the default .""" | template = self . resources . page . get ( 'image' )
return template . replace ( "{page}" , str ( page ) ) . replace ( "{size}" , "thumbnail" ) |
def to_json ( self , include_id : bool = False ) -> Mapping [ str , str ] :
"""Describe the namespaceEntry as dictionary of Namespace - Keyword and Name .
: param include _ id : If true , includes the model identifier""" | result = { NAMESPACE : self . namespace . keyword , }
if self . name :
result [ NAME ] = self . name
if self . identifier :
result [ IDENTIFIER ] = self . identifier
if include_id :
result [ 'id' ] = self . id
return result |
def _get_id_and_model ( self , id_or_model ) :
"""Get both the model and ID of an object that could be an ID or a model .
: param id _ or _ model :
The object that could be an ID string or a model object .
: param model _ collection :
The collection to which the model belongs .""" | if isinstance ( id_or_model , self . collection . model ) :
model = id_or_model
elif isinstance ( id_or_model , str ) : # Assume we have an ID string
model = self . collection . get ( id_or_model )
else :
raise TypeError ( 'Unexpected type {}, expected {} or {}' . format ( type ( id_or_model ) , str , self ... |
def _time_to_string ( self , dt , conversion_string = "%Y %m %d %H %M" ) :
"""This converts a UTC time integer to a string""" | if self . output_timezone is not None :
dt = dt . replace ( tzinfo = utc ) . astimezone ( self . output_timezone )
return dt . strftime ( conversion_string ) |
def add_input_data_to_scoped_data ( self , dictionary ) :
"""Add a dictionary to the scoped data
As the input _ data dictionary maps names to values , the functions looks for the proper data _ ports keys in the
input _ data _ ports dictionary
: param dictionary : The dictionary that is added to the scoped dat... | for dict_key , value in dictionary . items ( ) :
for input_data_port_key , data_port in list ( self . input_data_ports . items ( ) ) :
if dict_key == data_port . name :
self . scoped_data [ str ( input_data_port_key ) + self . state_id ] = ScopedData ( data_port . name , value , type ( value ) ,... |
def get_assessment_metadata ( self ) :
"""Gets the metadata for an assessment .
return : ( osid . Metadata ) - metadata for the assessment
* compliance : mandatory - - This method must be implemented . *""" | # Implemented from template for osid . resource . ResourceForm . get _ group _ metadata _ template
metadata = dict ( self . _mdata [ 'assessment' ] )
metadata . update ( { 'existing_id_values' : self . _my_map [ 'assessmentId' ] } )
return Metadata ( ** metadata ) |
def trees_by_issn ( self , issn ) :
"""Search trees by ` issn ` .
Args :
issn ( str ) : : attr : ` . Tree . issn ` property of : class : ` . Tree ` .
Returns :
set : Set of matching : class : ` Tree ` instances .""" | return set ( self . issn_db . get ( issn , OOSet ( ) ) . keys ( ) ) |
def resp_graph ( dataframe , image_name , dir = './' ) :
"""Response time graph for bucketed data
: param pandas . DataFrame dataframe : dataframe containing all data
: param str image _ name : the output file name
: param str dir : the output directory
: return : None""" | fig = pygal . TimeLine ( x_title = 'Elapsed Time In Test (secs)' , y_title = 'Response Time (secs)' , x_label_rotation = 25 , js = ( 'scripts/pygal-tooltip.min.js' , ) )
fig . add ( 'AVG' , [ ( get_local_time ( index ) , row [ 'mean' ] if pd . notnull ( row [ 'mean' ] ) else None ) for index , row in dataframe . iterro... |
def validate ( self ) :
"""Perform some basic checks to help ensure that the specification is valid .
Throws an exception if an invalid value is found .
Returns true if all checks were passed .
: return : boolean""" | # Check all values for None
for attr in self . __dict__ :
if self . __dict__ [ attr ] is None :
raise ValueError ( attr + " is not set" )
# Validate name
invalid_chars = GPTaskSpec . invalid_chars ( )
if any ( char in invalid_chars for char in self . name ) :
raise ValueError ( "module name includes inv... |
def _parse_dsn ( dsn ) :
"""Parse data source name .
This is a helper function to split the data source name provided in
the from _ dsn classmethod""" | conn_params = urlparse ( dsn )
init_args = { }
scheme_info = conn_params . scheme . split ( '+' )
if len ( scheme_info ) == 1 :
scheme = scheme_info [ 0 ]
modifier = None
else :
modifier , scheme = scheme_info
if scheme != 'influxdb' :
raise ValueError ( 'Unknown scheme "{0}".' . format ( scheme ) )
if ... |
def check_component_for_specific_sbo_term ( items , term ) :
r"""Identify model components that lack a specific SBO term ( s ) .
Parameters
items : list
A list of model components i . e . reactions to be checked for a specific
SBO term .
term : str or list of str
A string denoting a valid SBO term match... | # check for multiple allowable SBO terms
if isinstance ( term , list ) :
return [ elem for elem in items if elem . annotation is None or 'sbo' not in elem . annotation or not any ( i in elem . annotation [ 'sbo' ] for i in term ) ]
else :
return [ elem for elem in items if elem . annotation is None or 'sbo' not... |
def ipv4_public ( self , network = False , address_class = None ) :
"""Returns a public IPv4 excluding private blocks .
: param network : Network address
: param address _ class : IPv4 address class ( a , b , or c )
: returns : Public IPv4""" | # compute public networks
public_networks = [ _IPv4Constants . _network_classes [ address_class or self . ipv4_network_class ( ) ] ]
# exclude private and excluded special networks
public_networks = self . _exclude_ipv4_networks ( public_networks , _IPv4Constants . _private_networks + _IPv4Constants . _excluded_network... |
def netHours ( self ) :
'''For regular event staff , this is the net hours worked for financial purposes .
For Instructors , netHours is calculated net of any substitutes .''' | if self . specifiedHours is not None :
return self . specifiedHours
return self . event . duration - sum ( [ sub . netHours for sub in self . replacementFor . all ( ) ] ) |
def set_symbol ( self , symbol ) :
"""( symbol , bondorder ) - > set the bondsymbol
of the molecule""" | raise "Deprecated"
self . symbol , self . bondtype , bondorder , self . equiv_class = BONDLOOKUP [ symbol ]
if self . bondtype == 4 :
self . aromatic = 1
else :
self . aromatic = 0 |
def simplify ( cls , content_type ) :
"""The MIME types main - and sub - label can both start with < tt > x - < / tt > ,
which indicates that it is a non - registered name . Of course , after
registration this flag can disappear , adds to the confusing
proliferation of MIME types . The simplified string has t... | matchdata = MEDIA_TYPE_RE . match ( content_type )
if matchdata is None :
return None
wrap = lambda s : re . sub ( UNREG_RE , '' , s . lower ( ) )
( media_type , subtype ) = matchdata . groups ( )
return '%s/%s' % ( wrap ( media_type ) , wrap ( subtype ) ) |
def _parse_simple_model ( topology , parent_scope , model , inputs , outputs ) :
'''Parse a model containing only one operator ( aka simple model ) .
Steps :
1 . Create local scope for allocating local variables and operators
2 . Create operator and then feed the model ' s inputs and outputs to the operator
... | # Create local scope for the considered model
scope = topology . declare_scope ( 'single' , [ parent_scope ] + parent_scope . parent_scopes )
# Create operator for the considered model
this_operator = scope . declare_local_operator ( model . WhichOneof ( 'Type' ) , model )
# Allocate inputs for the operator and then co... |
def monitor ( self , operation = '' , ** kw ) :
""": returns : a new Monitor instance""" | mon = self . _monitor ( operation , hdf5 = self . datastore . hdf5 )
self . _monitor . calc_id = mon . calc_id = self . datastore . calc_id
vars ( mon ) . update ( kw )
return mon |
def _find_duplicates ( seq ) :
"""Find the duplicate elements from a sequence .""" | seen = set ( )
return [ element for element in seq if seq . count ( element ) > 1 and element not in seen and seen . add ( element ) is None ] |
def register ( coordinator ) :
"""Registers this module as a worker with the given coordinator .""" | utils . verify_binary ( 'pdiff_compare_binary' , [ '-version' ] )
utils . verify_binary ( 'pdiff_composite_binary' , [ '-version' ] )
assert FLAGS . pdiff_threads > 0
assert FLAGS . queue_server_prefix
item = queue_worker . RemoteQueueWorkflow ( constants . PDIFF_QUEUE_NAME , DoPdiffQueueWorkflow , max_tasks = FLAGS . ... |
def make_datetime ( value ) :
"""Tries to convert the given value to a : class : ` datetime . datetime ` . If
no timezone is given , raises a ValueError .
Strings will be parsed as ISO 8601 timestamps .
If a number is provided , it will be interpreted as a UNIX
timestamp , which by definition is UTC .
If ... | result = _make_datetime ( value )
if not result . tzinfo :
raise ValueError ( "value was a timestamp, but no timezone was set! " "Value was a '%s' object: %s" "\n\n" "Converted to naive 'datetime.datetime' object: %s" % ( value . __class__ . __name__ , repr ( value ) , repr ( result ) , ) )
return result |
def run ( self , line ) :
"""Extract words from tweet
1 . Remove non - ascii characters
2 . Split line into individual words
3 . Clean up puncuation characters""" | words = [ ]
for word in self . clean_unicode ( line . lower ( ) ) . split ( ) :
if word . startswith ( 'http' ) :
continue
cleaned = self . clean_punctuation ( word )
if len ( cleaned ) > 1 and cleaned not in self . stopwords :
words . append ( cleaned )
return words |
def clean ( self ) :
"""Remove all data by dropping and recreating the configured database .
. . note : :
Only the configured database is removed . Any other databases
remain untouched .""" | self . exec_pg_success ( [ 'dropdb' , '-U' , self . user , self . database ] )
self . exec_pg_success ( [ 'createdb' , '-U' , self . user , self . database ] ) |
def create_header ( self ) :
"""return CSP header dict""" | encapsulate = re . compile ( "|" . join ( [ '^self' , '^none' , '^unsafe-inline' , '^unsafe-eval' , '^sha[\d]+-[\w=-]+' , '^nonce-[\w=-]+' ] ) )
csp = { }
for p , array in self . inputs . items ( ) :
csp [ p ] = ' ' . join ( [ "'%s'" % l if encapsulate . match ( l ) else l for l in array ] )
return { self . header ... |
def align ( fastq_file , pair_file , index_dir , names , align_dir , data ) :
"""Perform piped alignment of fastq input files , generating sorted , deduplicated BAM .
Pipes in input , handling paired and split inputs , using interleaving magic
from : https : / / biowize . wordpress . com / 2015/03/26 / the - fa... | out_file = os . path . join ( align_dir , "{0}-sort.bam" . format ( dd . get_sample_name ( data ) ) )
num_cores = data [ "config" ] [ "algorithm" ] . get ( "num_cores" , 1 )
resources = config_utils . get_resources ( "snap" , data [ "config" ] )
rg_info = novoalign . get_rg_info ( names )
if data . get ( "align_split" ... |
async def save ( self , db = None ) :
'''If object has _ id , then object will be created or fully rewritten .
If not , object will be inserted and _ id will be assigned .''' | self . _db = db or self . db
data = self . prepare_data ( )
# validate object
self . validate ( )
# connect to DB to save the model
for i in self . connection_retries ( ) :
try :
created = False if '_id' in data else True
result = await self . db [ self . get_collection_name ( ) ] . insert_one ( dat... |
def patch ( ** on ) :
"""Globally patches certain system modules to be ' cooperaive ' .
The keyword arguments afford some control over which modules are patched .
If no keyword arguments are supplied , all possible modules are patched .
If keywords are set to True , only the specified modules are patched . E ... | accepted_args = set ( ( 'select' , 'socket' , 'time' ) )
default_on = on . pop ( "all" , None )
for k in on . keys ( ) :
if k not in accepted_args :
raise TypeError ( "patch() got an unexpected keyword argument %r" % k )
if default_on is None :
default_on = not ( True in list ( on . values ( ) ) )
for m... |
def communicate ( self ) :
"""Retrieve information .""" | self . _communicate_first = True
self . _process . waitForFinished ( )
enco = self . _get_encoding ( )
if self . _partial_stdout is None :
raw_stdout = self . _process . readAllStandardOutput ( )
stdout = handle_qbytearray ( raw_stdout , enco )
else :
stdout = self . _partial_stdout
raw_stderr = self . _pro... |
def show_vcs_output_vcs_nodes_vcs_node_info_node_swbd_number ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
show_vcs = ET . Element ( "show_vcs" )
config = show_vcs
output = ET . SubElement ( show_vcs , "output" )
vcs_nodes = ET . SubElement ( output , "vcs-nodes" )
vcs_node_info = ET . SubElement ( vcs_nodes , "vcs-node-info" )
node_swbd_number = ET . SubElement ( vcs_node_info , "node-swb... |
def previous_visit ( self ) :
"""Returns the previous visit for this request or None .
Requires attr ` visit _ model _ cls ` .""" | previous_visit = None
if self . appointment :
appointment = self . appointment
while appointment . previous_by_timepoint :
try :
previous_visit = self . model . visit_model_cls ( ) . objects . get ( appointment = appointment . previous_by_timepoint )
except ObjectDoesNotExist :
... |
def stop_capture ( self ) :
"""See base class documentation""" | if self . _process is None :
raise sniffer . InvalidOperationError ( "Trying to stop a non-started process" )
utils . stop_standing_subprocess ( self . _process , kill_signal = signal . SIGINT )
self . _post_process ( ) |
def create_mnist_model ( hyper_params , input_shape = ( H , W , 1 ) , num_classes = NUM_CLASSES ) :
'''Create simple convolutional model''' | layers = [ Conv2D ( 32 , kernel_size = ( 3 , 3 ) , activation = 'relu' , input_shape = input_shape ) , Conv2D ( 64 , ( 3 , 3 ) , activation = 'relu' ) , MaxPooling2D ( pool_size = ( 2 , 2 ) ) , Flatten ( ) , Dense ( 100 , activation = 'relu' ) , Dense ( num_classes , activation = 'softmax' ) ]
model = Sequential ( laye... |
def loads ( s : str , ** kwargs ) -> JsonObj :
"""Convert a json _ str into a JsonObj
: param s : a str instance containing a JSON document
: param kwargs : arguments see : json . load for details
: return : JsonObj representing the json string""" | if isinstance ( s , ( bytes , bytearray ) ) :
s = s . decode ( json . detect_encoding ( s ) , 'surrogatepass' )
return json . loads ( s , object_hook = lambda pairs : JsonObj ( ** pairs ) , ** kwargs ) |
def group_vectors ( vectors , angle = 1e-4 , include_negative = False ) :
"""Group vectors based on an angle tolerance , with the option to
include negative vectors .
Parameters
vectors : ( n , 3 ) float
Direction vector
angle : float
Group vectors closer than this angle in radians
include _ negative ... | vectors = np . asanyarray ( vectors , dtype = np . float64 )
angle = float ( angle )
if include_negative :
vectors = util . vector_hemisphere ( vectors )
spherical = util . vector_to_spherical ( vectors )
angles , groups = group_distance ( spherical , angle )
new_vectors = util . spherical_to_vector ( angles )
retu... |
def get_field_errors ( node ) :
"""return a list of FieldErrors if the specified securityData element has field errors""" | assert node . Name == 'securityData' and not node . IsArray
nodearr = node . GetElement ( 'fieldExceptions' )
if nodearr . NumValues > 0 :
secid = XmlHelper . get_child_value ( node , 'security' )
errors = XmlHelper . as_field_error ( nodearr , secid )
return errors
else :
return None |
def coroutine ( func : Callable [ ... , "Generator[Any, Any, _T]" ] ) -> Callable [ ... , "Future[_T]" ] :
"""Decorator for asynchronous generators .
For compatibility with older versions of Python , coroutines may
also " return " by raising the special exception ` Return ( value )
< Return > ` .
Functions ... | @ functools . wraps ( func )
def wrapper ( * args , ** kwargs ) : # type : ( * Any , * * Any ) - > Future [ _ T ]
# This function is type - annotated with a comment to work around
# https : / / bitbucket . org / pypy / pypy / issues / 2868 / segfault - with - args - type - annotation - in
future = _create_future ( ... |
def write ( self , offset , value ) :
""". . _ write :
Writes the memory word at ` ` offset ` ` to ` ` value ` ` .
Might raise ReadOnlyError _ , if the device is read - only .
Might raise AddressError _ , if the offset exceeds the size of the device .""" | if ( not self . mode & 0b10 ) :
raise ReadOnlyError ( "Device is Read-Only" )
if ( offset >= self . size ) :
raise AddressError ( "Offset({}) not in address space({})" . format ( offset , self . size ) )
self . repr_ [ offset ] . setvalue ( value ) |
def stansummary ( fit , pars = None , probs = ( 0.025 , 0.25 , 0.5 , 0.75 , 0.975 ) , digits_summary = 2 ) :
"""Summary statistic table .
Parameters
fit : StanFit4Model object
pars : str or sequence of str , optional
Parameter names . By default use all parameters
probs : sequence of float , optional
Qu... | if fit . mode == 1 :
return "Stan model '{}' is of mode 'test_grad';\n" "sampling is not conducted." . format ( fit . model_name )
elif fit . mode == 2 :
return "Stan model '{}' does not contain samples." . format ( fit . model_name )
n_kept = [ s - w for s , w in zip ( fit . sim [ 'n_save' ] , fit . sim [ 'war... |
def pip_uninstall ( package , ** options ) :
"""Uninstall a python package""" | command = [ "uninstall" , "-q" , "-y" ]
available_options = ( 'proxy' , 'log' , )
for option in parse_options ( options , available_options ) :
command . append ( option )
if isinstance ( package , list ) :
command . extend ( package )
else :
command . append ( package )
log ( "Uninstalling {} package with ... |
def parse ( el , typ ) :
"""Parse a ` ` BeautifulSoup ` ` element as the given type .""" | if not el :
return typ ( )
txt = text ( el )
if not txt :
return typ ( )
return typ ( txt ) |
def get_major_minor ( ilo_ver_str ) :
"""Extract the major and minor number from the passed string
: param ilo _ ver _ str : the string that contains the version information
: returns : String of the form " < major > . < minor > " or None""" | if not ilo_ver_str :
return None
try : # Note ( vmud213 ) : This logic works for all strings
# that contain the version info as < major > . < minor >
# Formats of the strings :
# Release version - > " 2.50 Feb 18 2016"
# Debug version - > " iLO 4 v2.50"
# random version - > " XYZ ABC 2.30"
pattern = re . search... |
def get_installed_apps ( ) :
"""Return list of all installed apps""" | if django . VERSION >= ( 1 , 7 ) :
from django . apps import apps
return [ a . models_module for a in apps . get_app_configs ( ) if a . models_module is not None ]
else :
from django . db import models
return models . get_apps ( ) |
def from_rfc3339 ( rfc3339_text , with_nanos = False ) :
"""Parse a RFC 3339 date string format to datetime . date .
Example of accepted format : ' 1972-01-01T10:00:20.021-05:00'
- By default , the result is a datetime . datetime
- If with _ nanos is true , the result is a 2 - tuple , ( datetime . datetime , ... | timestamp = strict_rfc3339 . rfc3339_to_timestamp ( rfc3339_text )
result = datetime . datetime . utcfromtimestamp ( timestamp )
if with_nanos :
return ( result , int ( ( timestamp - int ( timestamp ) ) * 1e9 ) )
else :
return result |
def feature_union ( names , steps , weights ) :
"""Reconstruct a FeatureUnion from names , steps , and weights""" | steps , times = zip ( * map ( _maybe_timed , steps ) )
fit_time = sum ( times )
if any ( s is FIT_FAILURE for s in steps ) :
fit_est = FIT_FAILURE
else :
fit_est = FeatureUnion ( list ( zip ( names , steps ) ) , transformer_weights = weights )
return fit_est , fit_time |
def stats ( self , topic = None , channel = None , text = False ) :
"""Return internal instrumented statistics .
: param topic : ( optional ) filter to topic
: param channel : ( optional ) filter to channel
: param text : return the stats as a string ( default : ` ` False ` ` )""" | if text :
fields = { 'format' : 'text' }
else :
fields = { 'format' : 'json' }
if topic :
nsq . assert_valid_topic_name ( topic )
fields [ 'topic' ] = topic
if channel :
nsq . assert_valid_channel_name ( channel )
fields [ 'channel' ] = channel
return self . _request ( 'GET' , '/stats' , fields ... |
def epcr_primer_file ( self , formattedprimers ) :
"""Create the ePCR - compatible primer file from the dictionaries of primer combinations""" | logging . info ( 'Creating re-PCR-compatible primer file' )
with open ( formattedprimers , 'w' ) as formatted : # Iterate through all the targets
for basename in sorted ( self . forward_dict ) : # Use enumerate to number the iterations for each forward and reverse primer in the lists
for forward_index , for... |
def pathwaysKEGG ( organism ) :
"""Retrieves all pathways for a given organism .
: param organism : an organism as listed in organismsKEGG ( )
: returns df : a Pandas dataframe with the columns ' KEGGid ' , ' pathIDs ' , and ' pathName ' .
: returns df _ : a Pandas dataframe with a columns for ' KEGGid ' , an... | print ( "KEGG API: http://rest.kegg.jp/list/pathway/" + organism )
sys . stdout . flush ( )
kegg_paths = urlopen ( "http://rest.kegg.jp/list/pathway/" + organism ) . read ( )
kegg_paths = kegg_paths . split ( "\n" )
final = [ ]
for k in kegg_paths :
final . append ( k . split ( "\t" ) )
df = pd . DataFrame ( final ... |
def DeleteAttachment ( self , attachment_link , options = None ) :
"""Deletes an attachment .
: param str attachment _ link :
The link to the attachment .
: param dict options :
The request options for the request .
: return :
The deleted Attachment .
: rtype :
dict""" | if options is None :
options = { }
path = base . GetPathFromLink ( attachment_link )
attachment_id = base . GetResourceIdOrFullNameFromLink ( attachment_link )
return self . DeleteResource ( path , 'attachments' , attachment_id , None , options ) |
def async_update ( self , event , reason = { } ) :
"""New event for sensor .
Check if state or config is part of event .
Signal that sensor has updated attributes .
Inform what attributes got changed values .""" | reason [ 'attr' ] = [ ]
for data in [ 'state' , 'config' ] :
changed_attr = self . update_attr ( event . get ( data , { } ) )
reason [ data ] = data in event
reason [ 'attr' ] += changed_attr
super ( ) . async_update ( event , reason ) |
def _filename ( self_or_cls , filename ) :
"Add the file extension if not already present" | if not filename . endswith ( self_or_cls . file_ext ) :
return '%s.%s' % ( filename , self_or_cls . file_ext )
else :
return filename |
def dataset_walker ( datasets ) :
"""Walk through * datasets * and their ancillary data .
Yields datasets and their parent .""" | for dataset in datasets :
yield dataset , None
for anc_ds in dataset . attrs . get ( 'ancillary_variables' , [ ] ) :
try :
anc_ds . attrs
yield anc_ds , dataset
except AttributeError :
continue |
def fire ( self , target , topic , content , callback = None ) :
"""Fires a message""" | message = self . __make_message ( topic , content )
if callback is not None :
self . __callbacks [ message [ 'uid' ] ] = ( 'fire' , callback )
self . __client . send_message ( target , json . dumps ( message ) , message [ 'uid' ] ) |
def _screaming_snake_case ( cls , text ) :
"""Transform text to SCREAMING _ SNAKE _ CASE
: param text :
: return :""" | if text . isupper ( ) :
return text
result = ''
for pos , symbol in enumerate ( text ) :
if symbol . isupper ( ) and pos > 0 :
result += '_' + symbol
else :
result += symbol . upper ( )
return result |
def analyze_quality_table ( self , obj , low_bound = None , high_bound = None ) :
"""Takes in an the object returned by the MDAL query , and analyzes the quality
of the data for each column in the df . Returns a df of data quality metrics
To Do
Need to make it specific for varying meters and label it for each... | data = obj . df
N_rows = 3
N_cols = data . shape [ 1 ]
d = pd . DataFrame ( np . zeros ( ( N_rows , N_cols ) ) , index = [ '% Missing' , 'AVG Length Missing' , 'Std dev. Missing' ] , columns = [ data . columns ] )
if low_bound :
data = data . where ( data >= low_bound )
if high_bound :
data = data . where ( dat... |
def set_eng_float_format ( accuracy = 3 , use_eng_prefix = False ) :
"""Alter default behavior on how float is formatted in DataFrame .
Format float in engineering format . By accuracy , we mean the number of
decimal digits after the floating point .
See also EngFormatter .""" | set_option ( "display.float_format" , EngFormatter ( accuracy , use_eng_prefix ) )
set_option ( "display.column_space" , max ( 12 , accuracy + 9 ) ) |
def post ( self , path , payload , callback = None , timeout = None , no_response = False , ** kwargs ) : # pragma : no cover
"""Perform a POST on a certain path .
: param path : the path
: param payload : the request payload
: param callback : the callback function to invoke upon response
: param timeout :... | request = self . mk_request ( defines . Codes . POST , path )
request . token = generate_random_token ( 2 )
request . payload = payload
if no_response :
request . add_no_response ( )
request . type = defines . Types [ "NON" ]
for k , v in kwargs . items ( ) :
if hasattr ( request , k ) :
setattr ( r... |
def GetHelper ( cls , type_indicator ) :
"""Retrieves the path specification resolver helper for the specified type .
Args :
type _ indicator ( str ) : type indicator .
Returns :
ResolverHelper : a resolver helper .
Raises :
KeyError : if resolver helper is not set for the corresponding type
indicator... | if type_indicator not in cls . _resolver_helpers :
raise KeyError ( 'Resolver helper not set for type indicator: {0:s}.' . format ( type_indicator ) )
return cls . _resolver_helpers [ type_indicator ] |
def get_vec_lr ( self ) :
"""Returns vector from left to right""" | return self . width * self . cos_a ( ) , - self . width * self . sin_a ( ) |
def random ( magnitude = 1 ) :
"""Create a unit vector pointing in a random direction .""" | theta = random . uniform ( 0 , 2 * math . pi )
return magnitude * Vector ( math . cos ( theta ) , math . sin ( theta ) ) |
def dispatch ( self , env ) :
"""very simple URL dispatch , a la Cake : / zelink maps to handle _ zelink""" | path = filter ( None , env [ 'PATH_INFO' ] . split ( '/' ) )
handler = getattr ( self , 'handle_%s' % path [ 0 ] , None )
if not handler :
return '404 Not Found' , '%(PATH_INFO)s not found' % env
return handler ( env ) |
def parse_buffer_to_png ( data ) :
"""Parse PNG file bytes to Pillow Image""" | images = [ ]
c1 = 0
c2 = 0
data_len = len ( data )
while c1 < data_len : # IEND can appear in a PNG without being the actual end
if data [ c2 : c2 + 4 ] == b'IEND' and ( c2 + 8 == data_len or data [ c2 + 9 : c2 + 12 ] == b'PNG' ) :
images . append ( Image . open ( BytesIO ( data [ c1 : c2 + 8 ] ) ) )
... |
def set_cursor_y ( self , y ) :
"""Set Screen Cursor Y Position""" | if y >= 0 and y <= self . server . server_info . get ( "screen_height" ) :
self . cursor_y = y
self . server . request ( "screen_set %s cursor_y %i" % ( self . ref , self . cursor_y ) ) |
def flip ( self , n_windows ) :
"""Flip the orientation of the page .""" | assert n_windows >= 0
self . page_index += ( self . step * n_windows )
self . cursor_index = n_windows
self . inverted = not self . inverted
self . top_item_height = None |
def GetTopLevel ( self , file_object ) :
"""Returns the deserialized content of a plist as a dictionary object .
Args :
file _ object ( dfvfs . FileIO ) : a file - like object to parse .
Returns :
dict [ str , object ] : contents of the plist .
Raises :
UnableToParseFile : when the file cannot be parsed... | try :
top_level_object = biplist . readPlist ( file_object )
except ( biplist . InvalidPlistException , biplist . NotBinaryPlistException ) as exception :
raise errors . UnableToParseFile ( 'Unable to parse plist with error: {0!s}' . format ( exception ) )
return top_level_object |
def get_parameter ( self ) :
"""Obtain list parameter object from the current widget state .
: returns : A DefaultValueParameter from the current state of widget
: rtype : DefaultValueParameter""" | # Set value for each key
for key , value in list ( self . _parameter . options . items ( ) ) :
if value . get ( 'type' ) == STATIC :
continue
elif value . get ( 'type' ) == SINGLE_DYNAMIC :
new_value = self . spin_boxes . get ( key ) . value ( )
self . _parameter . set_value_for_key ( ke... |
def _set_enable ( self , v , load = False ) :
"""Setter method for enable , mapped from YANG variable / beacon / enable ( container )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ enable is considered as a private
method . Backends looking to populate this variable ... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = enable . enable , is_container = 'container' , presence = False , yang_name = "enable" , rest_name = "enable" , parent = self , path_helper = self . _path_helper , extmethods = self . _extmethods , register_paths = True , ext... |
def Dir ( self , name , create = True ) :
"""Create a directory node named ' name ' relative to
the directory of this file .""" | return self . dir . Dir ( name , create = create ) |
def _get_annual_data ( self , p_p_id ) :
"""Get annual data .""" | params = { "p_p_id" : p_p_id , "p_p_lifecycle" : 2 , "p_p_state" : "normal" , "p_p_mode" : "view" , "p_p_resource_id" : "resourceObtenirDonneesConsommationAnnuelles" }
try :
raw_res = yield from self . _session . get ( PROFILE_URL , params = params , timeout = self . _timeout )
except OSError :
raise PyHydroQue... |
def options_string_builder ( option_mapping , args ) :
"""Return arguments for CLI invocation of kal .""" | options_string = ""
for option , flag in option_mapping . items ( ) :
if option in args :
options_string += str ( " %s %s" % ( flag , str ( args [ option ] ) ) )
return options_string |
def create_db ( self , instance_name , instance_type , admin_username , admin_password , security_groups = None , db_name = None , storage_size_gb = DEFAULT_STORAGE_SIZE_GB , timeout_s = DEFAULT_TIMEOUT_S ) :
"""Creates a database instance .
This method blocks until the db instance is active , or until
: attr :... | db = self . _create_db ( instance_name , instance_type , storage_size_gb )
# hang on to these . . . hpcloud only provides a way to generate a new
# set of username / password - there is no way to retrieve the originals .
default_creds = db . credential
log . debug ( 'Credentials for %s: %s' % ( instance_name , default_... |
def mkdir_p ( path ) :
"""mkdir - p path""" | if PY3 :
return os . makedirs ( path , exist_ok = True )
try :
os . makedirs ( path )
except OSError as exc :
if exc . errno == errno . EEXIST and os . path . isdir ( path ) :
pass
else :
raise |
def make_python_xref_nodes ( py_typestr , state , hide_namespace = False ) :
"""Make docutils nodes containing a cross - reference to a Python object .
Parameters
py _ typestr : ` str `
Name of the Python object . For example
` ` ' mypackage . mymodule . MyClass ' ` ` . If you have the object itself , or
... | if hide_namespace :
template = ':py:obj:`~{}`\n'
else :
template = ':py:obj:`{}`\n'
xref_text = template . format ( py_typestr )
return parse_rst_content ( xref_text , state ) |
def run ( self , server = None , host = None , port = None , enable_pretty_logging = True ) :
"""运行 WeRoBot 。
: param server : 传递给 Bottle 框架 run 方法的参数 , 详情见 ` bottle 文档 < https : / / bottlepy . org / docs / dev / deployment . html # switching - the - server - backend > ` _
: param host : 运行时绑定的主机地址
: param po... | if enable_pretty_logging :
from werobot . logger import enable_pretty_logging
enable_pretty_logging ( self . logger )
if server is None :
server = self . config [ "SERVER" ]
if host is None :
host = self . config [ "HOST" ]
if port is None :
port = self . config [ "PORT" ]
try :
self . wsgi . ru... |
async def query_firmware ( self ) :
"""Query the firmware versions .""" | _version = await self . request . get ( join_path ( self . _base_path , "/fwversion" ) )
_fw = _version . get ( "firmware" )
if _fw :
_main = _fw . get ( "mainProcessor" )
if _main :
self . _main_processor_version = self . _make_version ( _main )
_radio = _fw . get ( "radio" )
if _radio :
... |
def start ( transport = 'zmq' , address = '0.0.0.0' , port = 49017 , auth_address = '0.0.0.0' , auth_port = 49018 , disable_security = False , certificate = None , os_whitelist = None , os_blacklist = None , error_whitelist = None , error_blacklist = None , host_whitelist = None , host_blacklist = None ) :
'''Liste... | if not disable_security :
if not certificate :
log . critical ( 'Please use a certificate, or disable the security.' )
return
auth = napalm_logs . utils . ClientAuth ( certificate , address = auth_address , port = auth_port )
transport_recv_fun = _get_transport_recv ( name = transport , address ... |
def change_issue_status ( self , issue_id , status_id : str ) :
"""Смета статуса тикета
: param issue _ id : int
: param status _ id : int""" | self . __metadb . update ( """
update meta.issue set
issue_status_id=:status_id,
assignee_user_id=valera_user_id(),
last_user_id=valera_user_id()
where id = :issue_id
""" , { "issue_id" : issue_id , "status_id" : status_id } ) |
def initialize ( self ) :
"""Set window layout .""" | self . grid ( )
self . respond = ttk . Button ( self , text = 'Get Response' , command = self . get_response )
self . respond . grid ( column = 0 , row = 0 , sticky = 'nesw' , padx = 3 , pady = 3 )
self . usr_input = ttk . Entry ( self , state = 'normal' )
self . usr_input . grid ( column = 1 , row = 0 , sticky = 'nesw... |
def orthonormality ( V , ip_B = None ) :
"""Measure orthonormality of given basis .
: param V : a matrix : math : ` V = [ v _ 1 , \ ldots , v _ n ] ` with ` ` shape = = ( N , n ) ` ` .
: param ip _ B : ( optional ) the inner product to use , see : py : meth : ` inner ` .
: return : : math : ` \\ | I _ n - \\ ... | return norm ( numpy . eye ( V . shape [ 1 ] ) - inner ( V , V , ip_B = ip_B ) ) |
def create ( self , unique_name = values . unset , date_expiry = values . unset , ttl = values . unset , mode = values . unset , status = values . unset , participants = values . unset ) :
"""Create a new SessionInstance
: param unicode unique _ name : An application - defined string that uniquely identifies the ... | data = values . of ( { 'UniqueName' : unique_name , 'DateExpiry' : serialize . iso8601_datetime ( date_expiry ) , 'Ttl' : ttl , 'Mode' : mode , 'Status' : status , 'Participants' : serialize . map ( participants , lambda e : serialize . object ( e ) ) , } )
payload = self . _version . create ( 'POST' , self . _uri , da... |
def style_print ( * values , ** kwargs ) :
"""A convenience function that applies style _ format to text before printing""" | style = kwargs . pop ( "style" , None )
values = [ style_format ( value , style ) for value in values ]
print ( * values , ** kwargs ) |
def chunkComment ( self , text , start = 0 ) :
"""Return a list of chunks of comments .""" | # Build a list of comments
comm , out = self . nextComment ( text , start ) , [ ]
while comm :
out . append ( comm . group ( 0 ) )
comm = self . nextComment ( text , comm . start ( 0 ) + 1 )
# Collect the comments according to whether they are line
# comments or block comments .
out = [ list ( g ) for ( _ , g )... |
def _sysv_enabled ( name , root ) :
'''A System - V style service is assumed disabled if the " startup " symlink
( starts with " S " ) to its script is found in / etc / init . d in the current
runlevel .''' | # Find exact match ( disambiguate matches like " S01anacron " for cron )
rc = _root ( '/etc/rc{}.d/S*{}' . format ( _runlevel ( ) , name ) , root )
for match in glob . glob ( rc ) :
if re . match ( r'S\d{,2}%s' % name , os . path . basename ( match ) ) :
return True
return False |
def get_lockout_response ( self ) :
""": return :""" | return render_to_response ( self . template_name , { 'user_attempts' : self . last_attempt_instance , 'lockout_time' : self . block_login_seconds , 'ip_address' : self . ip } , context_instance = RequestContext ( self . request ) ) |
def _setsizes ( self , cursor = None ) :
"""Set stored input and output sizes for cursor execution .""" | if cursor is None :
cursor = self . _cursor
if self . _inputsizes :
cursor . setinputsizes ( self . _inputsizes )
for column , size in self . _outputsizes . items ( ) :
if column is None :
cursor . setoutputsize ( size )
else :
cursor . setoutputsize ( size , column ) |
def get_input ( prompt , default = None , choices = None , option_value = None ) :
"""If option _ value is not None , then return it . Otherwise get the result from
input .""" | if option_value is not None :
return option_value
choices = choices or [ ]
while 1 :
r = input ( prompt + ' ' ) . strip ( )
if not r and default is not None :
return default
if choices :
if r not in choices :
r = None
else :
break
else :
break
... |
def _rm_get_reference_coords_from_header ( parts ) :
"""extract the reference ( genomic sequence match ) coordinates of a repeat
occurrence from a repeatmakser header line . An example header line is : :
239 29.42 1.92 0.97 chr1 11 17 ( 41 ) C XX # YY ( 74 ) 104 1 m _ b1s502i1 4
the genomic start and end are ... | s = int ( parts [ 5 ] )
e = int ( parts [ 6 ] ) + 1
if ( s >= e ) :
raise AlignmentIteratorError ( "invalid repeatmakser header: " + " " . join ( parts ) )
return ( s , e ) |
def add ( self , X , y ) :
"""Add data about known tunable hyperparameter configurations and scores .
Refits model with all data .
Args :
X ( Union [ Dict [ str , object ] , List [ Dict [ str , object ] ] ] ) : dict or list of dicts of
hyperparameter combinations . Keys may only be the name of a tunable , a... | if isinstance ( X , dict ) :
X = [ X ]
y = [ y ]
# transform the list of dictionaries into a np array X _ raw
for i in range ( len ( X ) ) :
each = X [ i ]
# update best score and hyperparameters
if y [ i ] > self . _best_score :
self . _best_score = y [ i ]
self . _best_hyperparams ... |
def previous ( self ) :
"""Moves the ' Cursor ' to & returns the previous ' Node ' . Raises
' GameTreeEndError ' if the start of a branch is exceeded .""" | if self . index - 1 >= 0 : # more main line ?
self . index = self . index - 1
elif self . stack : # were we in a variation ?
self . gametree = self . stack . pop ( )
self . index = len ( self . gametree ) - 1
else :
raise GameTreeEndError
self . node = self . gametree [ self . index ]
self . nodenum = s... |
def slicing ( args , length ) :
"""Internally used .""" | if isinstance ( args , tuple ) :
for arg in args :
yield from slicing_singlevalue ( arg , length )
else :
yield from slicing_singlevalue ( args , length ) |
def _process ( self , input ) :
'''Takes in html - mixed body text as a string and returns a list of strings ,
lower case and with punctuation given spacing .
Called by self . _ gen _ sentence ( )
Args :
inpnut ( string ) : body text''' | input = re . sub ( "<[^>]*>" , " " , input )
punct = list ( string . punctuation )
for symbol in punct :
input = input . replace ( symbol , " %s " % symbol )
input = filter ( lambda x : x != u'' , input . lower ( ) . split ( ' ' ) )
return input |
def cursor ( self , offset = 0 , limit = None , order_by = None , as_dict = False ) :
"""See expression . fetch ( ) for input description .
: return : query cursor""" | if offset and limit is None :
raise DataJointError ( 'limit is required when offset is set' )
sql = self . make_sql ( )
if order_by is not None :
sql += ' ORDER BY ' + ', ' . join ( order_by )
if limit is not None :
sql += ' LIMIT %d' % limit + ( ' OFFSET %d' % offset if offset else "" )
logger . debug ( sq... |
def dup_finder ( file_path , directory = "." , enable_scandir = False ) :
"""Check a directory for duplicates of the specified file . This is meant
for a single file only , for checking a directory for dups , use
directory _ duplicates .
This is designed to be as fast as possible by doing lighter checks
bef... | size = os . path . getsize ( file_path )
if size == 0 :
for empty_file in remove_empty_files ( directory , dry_run = True ) :
yield empty_file
else :
with open ( file_path , 'rb' ) as f :
first_twenty = f . read ( 20 )
file_sha256 = file_hash ( file_path , "sha256" )
for root , directori... |
def recv ( self , nbytes ) :
"""Receive data from the channel . The return value is a string
representing the data received . The maximum amount of data to be
received at once is specified by C { nbytes } . If a string of length zero
is returned , the channel stream has closed .
@ param nbytes : maximum num... | try :
out = self . in_buffer . read ( nbytes , self . timeout )
except PipeTimeout , e :
raise socket . timeout ( )
ack = self . _check_add_window ( len ( out ) )
# no need to hold the channel lock when sending this
if ack > 0 :
m = Message ( )
m . add_byte ( chr ( MSG_CHANNEL_WINDOW_ADJUST ) )
m . ... |
def match_date ( self , value , strict = False ) :
"""if value is a date""" | value = stringify ( value )
try :
parse ( value )
except Exception :
self . shout ( 'Value %r is not a valid date' , strict , value ) |
def bin ( args ) :
"""% prog bin data . tsv
Conver tsv to binary format .""" | p = OptionParser ( bin . __doc__ )
p . add_option ( "--dtype" , choices = ( "float32" , "int32" ) , help = "dtype of the matrix" )
opts , args = p . parse_args ( args )
if len ( args ) != 1 :
sys . exit ( not p . print_help ( ) )
tsvfile , = args
dtype = opts . dtype
if dtype is None : # Guess
dtype = np . int3... |
def s3_bucket ( self ) :
"""Connect to the user defined Amazon S3 bucket .
Called on demand by : func : ` get ( ) ` and : func : ` put ( ) ` . Caches its
return value so that only a single connection is created .
: returns : A : class : ` boto . s3 . bucket . Bucket ` object .
: raises : : exc : ` . CacheBa... | if not hasattr ( self , 'cached_bucket' ) :
self . check_prerequisites ( )
with PatchedBotoConfig ( ) :
from boto . exception import BotoClientError , BotoServerError , S3ResponseError
# The following try / except block translates unexpected exceptions
# raised by Boto into a CacheBacken... |
def _reloader_child ( server , app , interval ) :
'''Start the server and check for modified files in a background thread .
As soon as an update is detected , KeyboardInterrupt is thrown in
the main thread to exit the server loop . The process exists with status
code 3 to request a reload by the observer proc... | lockfile = os . environ . get ( 'BOTTLE_LOCKFILE' )
bgcheck = FileCheckerThread ( lockfile , interval )
try :
bgcheck . start ( )
server . run ( app )
except KeyboardInterrupt :
pass
bgcheck . status , status = 5 , bgcheck . status
bgcheck . join ( )
# bgcheck . status = = 5 - - > silent exit
if status :
... |
def parse_bookmark_data ( data ) :
"""Return iterator for bookmarks of the form ( url , name , line number ) .
Bookmarks are not sorted .""" | name = None
lineno = 0
for line in data . splitlines ( ) :
lineno += 1
line = line . strip ( )
if line . startswith ( "NAME=" ) :
name = line [ 5 : ]
elif line . startswith ( "URL=" ) :
url = line [ 4 : ]
if url and name is not None :
yield ( url , name , lineno )
... |
def interpolate_single ( start , end , coefficient , how = 'linear' ) :
"""Interpolate single value between start and end in given number of steps""" | return INTERP_SINGLE_DICT [ how ] ( start , end , coefficient ) |
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