signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def blast ( args ) :
"""% prog blast < deltafile | coordsfile >
Covert delta or coordsfile to BLAST tabular output .""" | p = OptionParser ( blast . __doc__ )
opts , args = p . parse_args ( args )
if len ( args ) != 1 :
sys . exit ( not p . print_help ( ) )
deltafile , = args
blastfile = deltafile . rsplit ( "." , 1 ) [ 0 ] + ".blast"
if need_update ( deltafile , blastfile ) :
coords = Coords ( deltafile )
fw = open ( blastfil... |
def load_facts ( self , facts ) :
"""Load a set of facts into the CLIPS data base .
The C equivalent of the CLIPS load - facts command .
Facts can be loaded from a string or from a text file .""" | facts = facts . encode ( )
if os . path . exists ( facts ) :
ret = lib . EnvLoadFacts ( self . _env , facts )
if ret == - 1 :
raise CLIPSError ( self . _env )
else :
ret = lib . EnvLoadFactsFromString ( self . _env , facts , - 1 )
if ret == - 1 :
raise CLIPSError ( self . _env )
return r... |
def substitution_set ( string , indexes ) :
"""for a string , return a set of all possible substitutions""" | strlen = len ( string )
return { mutate_string ( string , x ) for x in indexes if valid_substitution ( strlen , x ) } |
def find_neighbor_pores ( self , pores , mode = 'union' , flatten = True , include_input = False ) :
r"""Returns a list of pores that are direct neighbors to the given pore ( s )
Parameters
pores : array _ like
Indices of the pores whose neighbors are sought
flatten : boolean
If ` ` True ` ` ( default ) t... | pores = self . _parse_indices ( pores )
if sp . size ( pores ) == 0 :
return sp . array ( [ ] , ndmin = 1 , dtype = int )
if 'lil' not in self . _am . keys ( ) :
self . get_adjacency_matrix ( fmt = 'lil' )
neighbors = topotools . find_neighbor_sites ( sites = pores , logic = mode , am = self . _am [ 'lil' ] , f... |
def load_plugins ( ) :
"""Loads all plugins specified in the RAFCON _ PLUGIN _ PATH environment variable""" | plugins = os . environ . get ( 'RAFCON_PLUGIN_PATH' , '' )
plugin_list = set ( plugins . split ( os . pathsep ) )
global plugin_dict
for plugin_path in plugin_list :
if not plugin_path :
continue
plugin_path = os . path . expandvars ( os . path . expanduser ( plugin_path ) ) . strip ( )
if not os . ... |
def collect_samples_straggler_mitigation ( agents , train_batch_size ) :
"""Collects at least train _ batch _ size samples .
This is the legacy behavior as of 0.6 , and launches extra sample tasks to
potentially improve performance but can result in many wasted samples .""" | num_timesteps_so_far = 0
trajectories = [ ]
agent_dict = { }
for agent in agents :
fut_sample = agent . sample . remote ( )
agent_dict [ fut_sample ] = agent
while num_timesteps_so_far < train_batch_size : # TODO ( pcm ) : Make wait support arbitrary iterators and remove the
# conversion to list here .
[ fu... |
def relative_filename_within_dir ( filename : str , directory : str ) -> str :
"""Starting with a ( typically absolute ) ` ` filename ` ` , returns the part of the
filename that is relative to the directory ` ` directory ` ` .
If the file is * not * within the directory , returns an empty string .""" | filename = os . path . abspath ( filename )
directory = os . path . abspath ( directory )
if os . path . commonpath ( [ directory , filename ] ) != directory : # Filename is not within directory
return ""
return os . path . relpath ( filename , start = directory ) |
def process_message ( self , message , * args , ** kwargs ) :
"""If its level is into persist levels , convert the message to models and save it""" | if not message . level in PERSISTENT_MESSAGE_LEVELS :
return message
user = kwargs . get ( "user" ) or self . get_user ( )
try :
anonymous = user . is_anonymous ( )
except TypeError :
anonymous = user . is_anonymous
if anonymous :
raise NotImplementedError ( 'Persistent message levels cannot be used for... |
def _extractEgaNegFromSent ( sentTokens , clausesDict , foundChains ) :
'''Meetod , mis tuvastab antud lausest ' ega ' - predikaadiga seotud eituse ( d ) : ega + sobiv verb .
* ) Juhtudel kui ' ega ' - le j2rgneb juba tuvastatud , positiivse polaarsusega verbiahel ( nt
ahel mille alguses on käskivas kõneviisi... | sonaEga = WordTemplate ( { ROOT : '^ega$' , POSTAG : '[DJ]' } )
verbEiJarel = WordTemplate ( { POSTAG : 'V' , FORM : '(o|nud|tud|nuks|nuvat|vat|ks|ta|taks|tavat)$' } )
verbEiJarel2 = WordTemplate ( { ROOT : '^mine$' , POSTAG : 'V' , FORM : 'neg o$' } )
verbTud = WordTemplate ( { POSTAG : 'V' , FORM : '(tud)$' } )
verb ... |
def run ( self ) :
"""run the plugin""" | parser = df_parser ( self . workflow . builder . df_path , workflow = self . workflow )
dockerfile_labels = parser . labels
labels = Labels ( dockerfile_labels )
component_label = labels . get_name ( Labels . LABEL_TYPE_COMPONENT )
try :
component = dockerfile_labels [ component_label ]
except KeyError :
raise ... |
def validate_po_files ( configuration , locale_dir , root_dir = None , report_empty = False , check_all = False ) :
"""Validate all of the po files found in the root directory that are not product of a merge .
Returns a boolean indicating whether or not problems were found .""" | found_problems = False
# List of . po files that are the product of a merge ( see generate . py ) .
merged_files = configuration . generate_merge . keys ( )
for dirpath , __ , filenames in os . walk ( root_dir if root_dir else locale_dir ) :
for name in filenames :
__ , ext = os . path . splitext ( name )
... |
def find_near_matches_substitutions ( subsequence , sequence , max_substitutions ) :
"""Find near - matches of the subsequence in the sequence .
This chooses a suitable fuzzy search implementation according to the given
parameters .
Returns a list of fuzzysearch . Match objects describing the matching parts
... | _check_arguments ( subsequence , sequence , max_substitutions )
if max_substitutions == 0 :
return [ Match ( start_index , start_index + len ( subsequence ) , 0 ) for start_index in search_exact ( subsequence , sequence ) ]
elif len ( subsequence ) // ( max_substitutions + 1 ) >= 3 :
return find_near_matches_su... |
def convert_to_cluster_template ( self , plugin_name , hadoop_version , template_name , filecontent ) :
"""Convert to cluster template
Create Cluster Template directly , avoiding Cluster Template
mechanism .""" | resp = self . api . post ( '/plugins/%s/%s/convert-config/%s' % ( plugin_name , hadoop_version , urlparse . quote ( template_name ) ) , data = filecontent )
if resp . status_code != 202 :
raise RuntimeError ( 'Failed to upload template file for plugin "%s"' ' and version "%s"' % ( plugin_name , hadoop_version ) )
e... |
def Tran ( m , x , rhol , rhog , mul , mug , sigma , D , roughness = 0 , L = 1 ) :
r'''Calculates two - phase pressure drop with the Tran ( 2000 ) correlation ,
also shown in [ 2 ] _ and [ 3 ] _ .
. . math : :
\ Delta P = dP _ { lo } \ phi _ { lo } ^ 2
. . math : :
\ phi _ { lo } ^ 2 = 1 + ( 4.3 \ Gamma ^... | # Liquid - only properties , for calculation of dP _ lo
v_lo = m / rhol / ( pi / 4 * D ** 2 )
Re_lo = Reynolds ( V = v_lo , rho = rhol , mu = mul , D = D )
fd_lo = friction_factor ( Re = Re_lo , eD = roughness / D )
dP_lo = fd_lo * L / D * ( 0.5 * rhol * v_lo ** 2 )
# Gas - only properties , for calculation of dP _ go
... |
def saveShp ( self , target ) :
"""Save an shp file .""" | if not hasattr ( target , "write" ) :
target = os . path . splitext ( target ) [ 0 ] + '.shp'
if not self . shapeType :
self . shapeType = self . _shapes [ 0 ] . shapeType
self . shp = self . __getFileObj ( target )
self . __shapefileHeader ( self . shp , headerType = 'shp' )
self . __shpRecords ( ) |
def _is_import_binding ( node , name , package = None ) :
"""Will reuturn node if node will import name , or node
will import * from package . None is returned otherwise .
See test cases for examples .""" | if node . type == syms . import_name and not package :
imp = node . children [ 1 ]
if imp . type == syms . dotted_as_names :
for child in imp . children :
if child . type == syms . dotted_as_name :
if child . children [ 2 ] . value == name :
return node
... |
def iter ( self ) :
"""Iterate over the sequences in self . file _ , yielding each as an
instance of the desired read class .
@ raise ValueError : If the input file has an odd number of records or
if any sequence has a different length than its predicted
secondary structure .""" | upperCase = self . _upperCase
for _file in self . _files :
with asHandle ( _file ) as fp :
records = SeqIO . parse ( fp , 'fasta' )
while True :
try :
record = next ( records )
except StopIteration :
break
try :
stru... |
def list_lbaas_l7policies ( self , retrieve_all = True , ** _params ) :
"""Fetches a list of all L7 policies for a listener .""" | return self . list ( 'l7policies' , self . lbaas_l7policies_path , retrieve_all , ** _params ) |
def add ( self , synchronous = True , ** kwargs ) :
"""Add provided Content View Component .
: param synchronous : What should happen if the server returns an HTTP
202 ( accepted ) status code ? Wait for the task to complete if
` ` True ` ` . Immediately return the server ' s response otherwise .
: param kw... | kwargs = kwargs . copy ( )
# shadow the passed - in kwargs
if 'data' not in kwargs : # data is required
kwargs [ 'data' ] = dict ( )
if 'component_ids' not in kwargs [ 'data' ] :
kwargs [ 'data' ] [ 'components' ] = [ _payload ( self . get_fields ( ) , self . get_values ( ) ) ]
kwargs . update ( self . _server_... |
def decode ( data ) :
"""Decode data employing some charset detection and including unicode BOM
stripping .""" | if isinstance ( data , unicode ) :
return data
# Detect standard unicode BOMs .
for bom , encoding in UNICODE_BOMS :
if data . startswith ( bom ) :
return data [ len ( bom ) : ] . decode ( encoding , errors = 'ignore' )
# Try straight UTF - 8.
try :
return data . decode ( 'utf-8' )
except UnicodeDec... |
def get_request ( profile , resource ) :
"""Do a GET request to Github ' s API .
Args :
profile
A profile generated from ` ` simplygithub . authentication . profile ` ` .
Such profiles tell this module ( i ) the ` ` repo ` ` to connect to ,
and ( ii ) the ` ` token ` ` to connect with .
resource
The p... | url = get_url ( profile , resource )
headers = get_headers ( profile )
response = requests . get ( url , headers = headers )
return response . json ( ) |
def get_container_containers ( self , path ) :
""": param path : str or Path instance
: return :
: rtype : dict [ str , ValueTree ]
: raises ValueError : A component of path is a field name .
: raises KeyError : A component of path doesn ' t exist .""" | container = self . get_container ( path )
containers = { }
for name , value in container . _values . items ( ) :
if isinstance ( value , ValueTree ) :
containers [ name ] = value
return containers |
async def set_agent ( self , msg , context ) :
"""Mark a client as the RPC agent for a service .""" | service = msg . get ( 'name' )
client = context . user_data
self . service_manager . set_agent ( service , client ) |
def tree ( self , level = 0 , prefix = '' ) :
"""A string representation of the tree rooted in this node , useful for
debugging purposes .""" | text = '%s%s\n' % ( prefix , self . value . text )
prefix = '%s└── ' % ( ' ' * level )
if self . _lesser :
text += self . _lesser . tree ( level + 1 , prefix )
if self . _greater :
text += self . _greater . tree ( level + 1 , prefix )
return text |
def page_erase ( addr ) :
"""Erases a single page .""" | if __verbose :
print ( "Erasing page: 0x%x..." % ( addr ) )
# Send DNLOAD with first byte = 0x41 and page address
buf = struct . pack ( "<BI" , 0x41 , addr )
__dev . ctrl_transfer ( 0x21 , __DFU_DNLOAD , 0 , __DFU_INTERFACE , buf , __TIMEOUT )
# Execute last command
if get_status ( ) != __DFU_STATE_DFU_DOWNLOAD_BUS... |
def dict2obj ( d ) :
"""A helper function which convert a dict to an object .""" | if isinstance ( d , ( list , tuple ) ) :
d = [ dict2obj ( x ) for x in d ]
if not isinstance ( d , dict ) :
return d
class ObjectFromDict ( object ) :
pass
o = ObjectFromDict ( )
# an object created from a dict
for k in d :
o . __dict__ [ k ] = dict2obj ( d [ k ] )
return o |
def _view_filter ( self ) :
"""Overrides OsidSession . _ view _ filter to add sequestering filter .""" | view_filter = OsidSession . _view_filter ( self )
if self . _sequestered_view == SEQUESTERED :
view_filter [ 'sequestered' ] = False
return view_filter |
def _parse_dependencies ( self , pmodules , dependencies , recursive , greedy ) :
"""Parses the dependencies of the modules in the list pmodules .
: arg pmodules : a list of modules that were parsed from a * . f90 file .
: arg dependencies : when true , the dependency ' s dependencies will be loaded .
: arg r... | # See if we need to also load dependencies for the modules
if dependencies :
allkeys = [ module . name . lower ( ) for module in pmodules ]
for key in allkeys :
for depend in self . modules [ key ] . collection ( "dependencies" ) :
base = depend . split ( "." ) [ 0 ]
if self . ve... |
def rargmax ( x , eps = 1e-8 ) :
"""Argmax with random tie - breaking
Args :
x : a 1 - dim numpy array
Returns :
the argmax index""" | idxs = np . where ( abs ( x - np . max ( x , axis = 0 ) ) < eps ) [ 0 ]
return np . random . choice ( idxs ) |
def process_value ( self , value ) :
"""Process publication value""" | # UID - > SuperModel
if api . is_uid ( value ) :
return self . to_super_model ( value )
# Content - > SuperModel
elif api . is_object ( value ) :
return self . to_super_model ( value )
# String - > Unicode
elif isinstance ( value , basestring ) :
return safe_unicode ( value ) . encode ( "utf-8" )
# DateTime... |
def _parseKeyNames ( lib ) :
"""returns a dictionary mapping of human readable key names to their keycodes
this parses constants with the names of K _ * and makes code = name pairs
this is for KeyEvent . key variable and that enables things like :
if ( event . key = = ' PAGEUP ' ) :""" | _keyNames = { }
for attr in dir ( lib ) : # from the modules variables
if attr [ : 6 ] == 'TCODK_' : # get the K _ * constants
_keyNames [ getattr ( lib , attr ) ] = attr [ 6 : ]
# and make CODE = NAME pairs
return _keyNames |
def get_precinctsreportingpct ( self , obj ) :
"""Precincts reporting percent if vote is top level result else ` ` None ` ` .""" | if obj . division . level == obj . candidate_election . election . division . level :
return obj . candidate_election . election . meta . precincts_reporting_pct
return None |
def destroy ( self , request , project , pk = None ) :
"""Delete a note entry""" | try :
note = JobNote . objects . get ( id = pk )
note . delete ( )
return Response ( { "message" : "Note deleted" } )
except JobNote . DoesNotExist :
return Response ( "No note with id: {0}" . format ( pk ) , status = HTTP_404_NOT_FOUND ) |
def is_name_zonefile_hash ( self , name , zonefile_hash ) :
"""Was a zone file sent by a name ?""" | cur = self . db . cursor ( )
return namedb_is_name_zonefile_hash ( cur , name , zonefile_hash ) |
def get_temperature ( self ) :
"""Returns the current environment temperature .
Attention : Returns None if the value can ' t be queried or is unknown .""" | # raise NotImplementedError ( " This should work according to the AVM docs , but don ' t . . . " )
value = self . box . homeautoswitch ( "gettemperature" , self . actor_id )
if value . isdigit ( ) :
self . temperature = float ( value ) / 10
else :
self . temperature = None
return self . temperature |
def parse ( self , xml_file ) :
"Get a list of parsed recipes from BeerXML input" | recipes = [ ]
with open ( xml_file , "rt" ) as f :
tree = ElementTree . parse ( f )
for recipeNode in tree . iter ( ) :
if self . to_lower ( recipeNode . tag ) != "recipe" :
continue
recipe = Recipe ( )
recipes . append ( recipe )
for recipeProperty in list ( recipeNode ) :
tag_name ... |
def set_text ( self , text = None , ** kwargs ) :
"""Add textual information passed as dictionary .
All pairs in dictionary will be written , but keys should be latin - 1;
registered keywords could be used as arguments .
When called more than once overwrite exist data .""" | if text is None :
text = { }
text . update ( popdict ( kwargs , _registered_kw ) )
if 'Creation Time' in text and not isinstance ( text [ 'Creation Time' ] , ( basestring , bytes ) ) :
text [ 'Creation Time' ] = datetime . datetime ( * ( check_time ( text [ 'Creation Time' ] ) [ : 6 ] ) ) . isoformat ( )
self .... |
def execute_command ( self , * args , ** options ) :
"""Execute a command and return a parsed response .""" | pool = self . connection_pool
command_name = args [ 0 ]
connection = pool . get_connection ( command_name , ** options )
try :
connection . send_command ( * args )
return self . parse_response ( connection , command_name , ** options )
except ConnectionError :
connection . disconnect ( )
connection . se... |
def safecall ( func ) :
"""Wraps a function so that it swallows exceptions .""" | def wrapper ( * args , ** kwargs ) :
try :
return func ( * args , ** kwargs )
except Exception :
pass
return wrapper |
def attach_profile_to_role ( client , role_name = 'forrest_unicorn_role' , profile_name = 'forrest_unicorn_profile' ) :
"""Attach an IAM Instance Profile _ profile _ name _ to Role _ role _ name _ .
Args :
role _ name ( str ) : Name of Role .
profile _ name ( str ) : Name of Instance Profile .
Returns :
T... | current_instance_profiles = resource_action ( client , action = 'list_instance_profiles_for_role' , log_format = 'Found Instance Profiles for %(RoleName)s.' , RoleName = role_name ) [ 'InstanceProfiles' ]
for profile in current_instance_profiles :
if profile [ 'InstanceProfileName' ] == profile_name :
LOG .... |
def filenames ( self ) :
"""A list of all handled auxiliary file names .
> > > from hydpy import dummies
> > > dummies . v2af . filenames
[ ' file1 ' , ' file2 ' ]""" | fns = set ( )
for fn2var in self . _type2filename2variable . values ( ) :
fns . update ( fn2var . keys ( ) )
return sorted ( fns ) |
def on_api_error ( self , error_status = None , message = None , event_origin = None ) :
"""API error handling""" | if message . meta [ "error" ] . find ( "Widget instance not found on server" ) > - 1 : # widget is missing on the other side , try to re - attach
# then try again
error_status [ "retry" ] = True
self . comm . attach_remote ( self . id , self . remote_name , remote_name = self . name , ** self . init_kwargs ) |
def compute_process_sigmas ( self , dt , fx = None , ** fx_args ) :
"""computes the values of sigmas _ f . Normally a user would not call
this , but it is useful if you need to call update more than once
between calls to predict ( to update for multiple simultaneous
measurements ) , so the sigmas correctly re... | if fx is None :
fx = self . fx
# calculate sigma points for given mean and covariance
sigmas = self . points_fn . sigma_points ( self . x , self . P )
for i , s in enumerate ( sigmas ) :
self . sigmas_f [ i ] = fx ( s , dt , ** fx_args ) |
def get_name_levels ( node ) :
"""Return a list of ` ` ( name , level ) ` ` tuples for assigned names
The ` level ` is ` None ` for simple assignments and is a list of
numbers for tuple assignments for example in : :
a , ( b , c ) = x
The levels for for ` a ` is ` ` [ 0 ] ` ` , for ` b ` is ` ` [ 1 , 0 ] ` ... | visitor = _NodeNameCollector ( )
ast . walk ( node , visitor )
return visitor . names |
def get_server_session ( self ) :
"""Start or resume a server session , or raise ConfigurationError .""" | with self . _lock :
session_timeout = self . _description . logical_session_timeout_minutes
if session_timeout is None : # Maybe we need an initial scan ? Can raise ServerSelectionError .
if self . _description . topology_type == TOPOLOGY_TYPE . Single :
if not self . _description . has_know... |
def load_script ( self , source_name , timeoutMilliseconds = 0 ) :
"""Return ScriptHook for source _ name Source and with a ready timeout
of timeoutMilliseconds""" | script_path = os . path . join ( self . scripts_dir_path , self . _source_to_script_name ( source_name ) )
if os . path . isfile ( script_path ) :
return ScriptHook ( script_path , timeoutMilliseconds )
return None |
def send ( token_hex , message , ** kwargs ) :
"""Site : https : / / apple . com
API : https : / / developer . apple . com
Desc : iOS notifications
Installation and usage :
pip install hyper""" | priority = kwargs . pop ( 'priority' , 10 )
topic = kwargs . pop ( 'topic' , None )
alert = { "title" : kwargs . pop ( "event" ) , "body" : message , "action" : kwargs . pop ( 'apns_action' , defaults . APNS_PROVIDER_DEFAULT_ACTION ) }
data = { "aps" : { 'alert' : alert , 'content-available' : kwargs . pop ( 'content_a... |
def department ( self ) :
"""| Description : The ID of the department to which the chat is directed""" | if self . api and self . department_id :
return self . api . _get_department ( self . department_id ) |
def _set_ext_vni_any ( self , v , load = False ) :
"""Setter method for ext _ vni _ any , mapped from YANG variable / overlay / access _ list / type / vxlan / extended / ext _ seq / ext _ vni _ any ( empty )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ ext _ vni _ an... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = YANGBool , is_leaf = True , yang_name = "ext-vni-any" , rest_name = "vni-any" , parent = self , choice = ( u'choice-ext-vni' , u'case-ext-vni-any' ) , path_helper = self . _path_helper , extmethods = self . _extmethods , regi... |
def t_WSIGNORE_comment ( self , token ) :
r'[ # ] [ ^ \ n ] * \ n +' | token . lexer . lineno += token . value . count ( '\n' )
newline_token = _create_token ( 'NEWLINE' , '\n' , token . lineno , token . lexpos + len ( token . value ) - 1 )
newline_token . lexer = token . lexer
self . _check_for_indent ( newline_token ) |
def gpg_profile_put_key ( blockchain_id , key_id , key_name = None , immutable = True , txid = None , key_url = None , use_key_server = True , key_server = None , proxy = None , wallet_keys = None , gpghome = None ) :
"""Put a local GPG key into a blockchain ID ' s global account .
If the URL is not given , the k... | if key_name is not None :
assert is_valid_keyname ( key_name )
if key_server is None :
key_server = DEFAULT_KEY_SERVER
if gpghome is None :
gpghome = get_default_gpg_home ( )
put_res = { }
extra_fields = { }
key_data = None
if key_name is not None :
extra_fields = { 'keyName' : key_name }
if key_url is ... |
def aln_tree_seqs ( seqs , input_handler = None , tree_type = 'neighborjoining' , params = { } , add_seq_names = True , WorkingDir = tempfile . gettempdir ( ) , SuppressStderr = None , SuppressStdout = None , max_hours = 5.0 , constructor = PhyloNode , clean_up = True ) :
"""Muscle align sequences and report tree f... | params [ "-maxhours" ] = max_hours
if tree_type :
params [ "-cluster2" ] = tree_type
params [ "-tree2" ] = get_tmp_filename ( WorkingDir )
params [ "-out" ] = get_tmp_filename ( WorkingDir )
muscle_res = muscle_seqs ( seqs , input_handler = input_handler , params = params , add_seq_names = add_seq_names , WorkingDi... |
def v_res ( self , nodes = None , level = None ) :
"""Get resulting voltage level at node .
Parameters
nodes : : obj : ` list `
List of string representatives of grid topology components , e . g .
: class : ` ~ . grid . components . Generator ` . If not provided defaults to
all nodes available in grid lev... | # check if voltages are available :
if hasattr ( self , 'pfa_v_mag_pu' ) :
self . pfa_v_mag_pu . sort_index ( axis = 1 , inplace = True )
else :
message = "No voltage results available."
raise AttributeError ( message )
if level is None :
level = [ 'mv' , 'lv' ]
if nodes is None :
return self . pfa_... |
def _minimize_scalar ( self , desc = "Progress" , rtol = 1.4902e-08 , atol = 1.4902e-08 , verbose = True ) :
"""Minimize a scalar function using Brent ' s method .
Parameters
verbose : bool
` ` True ` ` for verbose output ; ` ` False ` ` otherwise .""" | from tqdm import tqdm
from numpy import asarray
from brent_search import minimize as brent_minimize
variables = self . _variables . select ( fixed = False )
if len ( variables ) != 1 :
raise ValueError ( "The number of variables must be equal to one." )
var = variables [ variables . names ( ) [ 0 ] ]
progress = tqd... |
def serve ( host , port , app , request_handler , error_handler , before_start = None , after_start = None , before_stop = None , after_stop = None , debug = False , request_timeout = 60 , response_timeout = 60 , keep_alive_timeout = 5 , ssl = None , sock = None , request_max_size = None , request_buffer_queue_size = 1... | if not run_async : # create new event _ loop after fork
loop = asyncio . new_event_loop ( )
asyncio . set_event_loop ( loop )
if debug :
loop . set_debug ( debug )
connections = connections if connections is not None else set ( )
server = partial ( protocol , loop = loop , connections = connections , signal... |
def get_plane_equation ( p0 , p1 , p2 , reference ) :
'''Define the equation of target fault plane passing through 3 given points
which includes two points on the fault trace and one point on the
fault plane but away from the fault trace . Note : in order to remain the
consistency of the fault normal vector d... | p0_xyz = get_xyz_from_ll ( p0 , reference )
p1_xyz = get_xyz_from_ll ( p1 , reference )
p2_xyz = get_xyz_from_ll ( p2 , reference )
p0 = np . array ( p0_xyz )
p1 = np . array ( p1_xyz )
p2 = np . array ( p2_xyz )
u = p1 - p0
v = p2 - p0
# vector normal to plane , ax + by + cy = d , normal = ( a , b , c )
normal = np . ... |
def from_spectrogram ( cls , * spectrograms , ** kwargs ) :
"""Calculate a new ` SpectralVariance ` from a
: class : ` ~ gwpy . spectrogram . Spectrogram `
Parameters
spectrogram : ` ~ gwpy . spectrogram . Spectrogram `
input ` Spectrogram ` data
bins : ` ~ numpy . ndarray ` , optional
array of histogra... | # parse args and kwargs
if not spectrograms :
raise ValueError ( "Must give at least one Spectrogram" )
bins = kwargs . pop ( 'bins' , None )
low = kwargs . pop ( 'low' , None )
high = kwargs . pop ( 'high' , None )
nbins = kwargs . pop ( 'nbins' , 500 )
log = kwargs . pop ( 'log' , False )
norm = kwargs . pop ( 'n... |
def avg_send_rate ( self ) :
"""Average sending rate in MB / s over the entire run . This data may
not exist if iperf was interrupted .
If the result is not from a success run , this property is None .""" | if not self . _has_data or 'sum_sent' not in self . result [ 'end' ] :
return None
bps = self . result [ 'end' ] [ 'sum_sent' ] [ 'bits_per_second' ]
return bps / 8 / 1024 / 1024 |
def flash_size_bytes ( size ) :
"""Given a flash size of the type passed in args . flash _ size
( ie 512KB or 1MB ) then return the size in bytes .""" | if "MB" in size :
return int ( size [ : size . index ( "MB" ) ] ) * 1024 * 1024
elif "KB" in size :
return int ( size [ : size . index ( "KB" ) ] ) * 1024
else :
raise FatalError ( "Unknown size %s" % size ) |
def _string_from_cmd_list ( cmd_list ) :
"""Takes a list of command line arguments and returns a pretty
representation for printing .""" | cl = [ ]
for arg in map ( str , cmd_list ) :
if ' ' in arg or '\t' in arg :
arg = '"' + arg + '"'
cl . append ( arg )
return ' ' . join ( cl ) |
def _set_local_node ( self , v , load = False ) :
"""Setter method for local _ node , mapped from YANG variable / local _ node ( container )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ local _ node is considered as a private
method . Backends looking to populate t... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = local_node . local_node , is_container = 'container' , presence = False , yang_name = "local-node" , rest_name = "local-node" , parent = self , path_helper = self . _path_helper , extmethods = self . _extmethods , register_pa... |
def set_inlets ( self , pores = None , clusters = None ) :
r"""Parameters
pores : array _ like
The list of inlet pores from which the Phase can enter the Network
clusters : list of lists - can be just one list but each list defines
a cluster of pores that share a common invasion pressure .
Like Basic Inva... | if pores is not None :
logger . info ( "Setting inlet pores at shared pressure" )
clusters = [ ]
clusters . append ( pores )
elif clusters is not None :
logger . info ( "Setting inlet clusters at individual pressures" )
else :
logger . error ( "Either 'inlets' or 'clusters' must be passed to" + " se... |
def parse ( self ) :
"""Parse the table data string into records .""" | self . parse_fields ( )
records = [ ]
for line in self . t [ 'data' ] . split ( '\n' ) :
if EMPTY_ROW . match ( line ) :
continue
row = [ self . autoconvert ( line [ start_field : end_field + 1 ] ) for start_field , end_field in self . fields ]
records . append ( tuple ( row ) )
self . records = rec... |
def setWorkingSeatedZeroPoseToRawTrackingPose ( self ) :
"""Sets the preferred seated position in the working copy .""" | fn = self . function_table . setWorkingSeatedZeroPoseToRawTrackingPose
pMatSeatedZeroPoseToRawTrackingPose = HmdMatrix34_t ( )
fn ( byref ( pMatSeatedZeroPoseToRawTrackingPose ) )
return pMatSeatedZeroPoseToRawTrackingPose |
def getPrioritySortkey ( self ) :
"""Returns the key that will be used to sort the current Analysis
Request based on both its priority and creation date . On ASC sorting ,
the oldest item with highest priority will be displayed .
: return : string used for sorting""" | priority = self . getPriority ( )
created_date = self . created ( ) . ISO8601 ( )
return '%s.%s' % ( priority , created_date ) |
def segment_text ( text = os . path . join ( DATA_PATH , 'goodreads-omniscient-books.txt' ) , start = None , stop = r'^Rate\ this' , ignore = r'^[\d]' ) :
"""Split text into segments ( sections , paragraphs ) using regular expressions to trigger breaks . start""" | start = start if hasattr ( start , 'match' ) else re . compile ( start ) if start else None
stop = stop if hasattr ( stop , 'match' ) else re . compile ( stop ) if stop else None
ignore = ignore if hasattr ( ignore , 'match' ) else re . compile ( ignore ) if ignore else None
segments = [ ]
segment = [ ]
with open ( tex... |
def _check_valid_label ( self , label ) :
"""Validate label and its shape .""" | if len ( label . shape ) != 2 or label . shape [ 1 ] < 5 :
msg = "Label with shape (1+, 5+) required, %s received." % str ( label )
raise RuntimeError ( msg )
valid_label = np . where ( np . logical_and ( label [ : , 0 ] >= 0 , label [ : , 3 ] > label [ : , 1 ] , label [ : , 4 ] > label [ : , 2 ] ) ) [ 0 ]
if v... |
def do_loop_turn ( self ) : # pylint : disable = too - many - branches
"""Satellite main loop : :
* Check and delete zombies actions / modules
* Get returns from queues
* Adjust worker number
* Get new actions
: return : None""" | # Try to see if one of my module is dead , and restart previously dead modules
self . check_and_del_zombie_modules ( )
# Also if some zombie workers exist . . .
self . check_and_del_zombie_workers ( )
# Call modules that manage a starting tick pass
self . hook_point ( 'tick' )
# Print stats for debug
for _ , sched in s... |
def save ( self , filename ) :
"""Save model to pickle file . External feature function is not stored""" | import dill
tmpmodelparams = self . modelparams . copy ( )
# fv _ extern _ src = None
fv_extern_name = None
# try :
# fv _ extern _ src = dill . source . getsource ( tmpmodelparams [ ' fv _ extern ' ] )
# tmpmodelparams . pop ( ' fv _ extern ' )
# except :
# pass
# fv _ extern _ name = dill . source . getname ( tmpmode... |
def _commit ( self ) :
"""Commits the batch .
This is called by : meth : ` commit ` .""" | if self . _id is None :
mode = _datastore_pb2 . CommitRequest . NON_TRANSACTIONAL
else :
mode = _datastore_pb2 . CommitRequest . TRANSACTIONAL
commit_response_pb = self . _client . _datastore_api . commit ( self . project , mode , self . _mutations , transaction = self . _id )
_ , updated_keys = _parse_commit_r... |
def refresh ( self ) :
"""* * refresh * *
Refresh this user object with data from the Gett service
Input :
* None
Output :
* ` ` True ` `
Example : :
if client . user . refresh ( ) :
print " User data refreshed ! "
print " You have % s bytes of storage remaining . " % ( client . user . storage _ l... | response = GettRequest ( ) . get ( "/users/me?accesstoken=%s" % self . access_token ( ) )
if response . http_status == 200 :
self . userid = response . response [ 'userid' ]
self . fullname = response . response [ 'fullname' ]
self . storage_used = response . response [ 'storage' ] [ 'used' ]
self . sto... |
def mod_repo ( repo , saltenv = 'base' , ** kwargs ) :
'''Modify one or more values for a repo . If the repo does not exist , it will
be created , so long as the definition is well formed . For Ubuntu the
` ` ppa : < project > / repo ` ` format is acceptable . ` ` ppa : ` ` format can only be
used to create a... | if 'refresh_db' in kwargs :
salt . utils . versions . warn_until ( 'Neon' , 'The \'refresh_db\' argument to \'pkg.mod_repo\' has been ' 'renamed to \'refresh\'. Support for using \'refresh_db\' will be ' 'removed in the Neon release of Salt.' )
refresh = kwargs [ 'refresh_db' ]
else :
refresh = kwargs . get... |
def x ( * args , ** kwargs ) :
'''same as sys . exit ( 1 ) but prints out where it was called from before exiting
I just find this really handy for debugging sometimes
since - - 2013-5-9
exit _ code - - int - - if you want it something other than 1''' | with Reflect . context ( args , ** kwargs ) as r :
instance = V_CLASS ( r , stream , ** kwargs )
if args :
instance ( )
else :
instance . writelines ( [ 'exit at line {}\n' . format ( instance . reflect . info [ "line" ] ) , instance . path_value ( ) ] )
exit_code = 1
sys . exit ( exit_code ... |
def get_dem ( bounds , out_file = "dem.tif" , src_crs = "EPSG:3005" , dst_crs = "EPSG:3005" , resolution = 25 ) :
"""Get 25m DEM for provided bounds , write to GeoTIFF""" | bbox = "," . join ( [ str ( b ) for b in bounds ] )
# todo : validate resolution units are equivalent to src _ crs units
# build request
payload = { "service" : "WCS" , "version" : "1.0.0" , "request" : "GetCoverage" , "coverage" : "pub:bc_elevation_25m_bcalb" , "Format" : "GeoTIFF" , "bbox" : bbox , "CRS" : src_crs , ... |
def convenience_calc_hessian ( self , params ) :
"""Calculates the hessian of the log - likelihood for this model / dataset .
Note that this function name is INCORRECT with regard to the actual
actions performed . The Mixed Logit model uses the BHHH approximation
to the Fisher Information Matrix in place of t... | shapes , intercepts , betas = self . convenience_split_params ( params )
args = [ betas , self . design_3d , self . alt_id_vector , self . rows_to_obs , self . rows_to_alts , self . rows_to_mixers , self . choice_vector , self . utility_transform ]
approx_hess = general_bhhh ( * args , ridge = self . ridge , weights = ... |
def _print_p ( self ) :
"""m . _ print _ p ( ) - - Print probability ( frequency ) matrix""" | print "# " ,
for i in range ( self . width ) :
print " %4d " % i ,
print
for L in [ 'A' , 'C' , 'T' , 'G' ] :
print "#%s " % L ,
for i in range ( self . width ) :
print "%8.3f " % math . pow ( 2 , self . logP [ i ] [ L ] ) ,
print |
def arg_to_dict ( arg ) :
"""Convert an argument that can be None , list / tuple or dict to dict
Example : :
> > > arg _ to _ dict ( None )
> > > arg _ to _ dict ( [ ' a ' , ' b ' ] )
{ ' a ' : { } , ' b ' : { } }
> > > arg _ to _ dict ( { ' a ' : { ' only ' : ' id ' } , ' b ' : { ' only ' : ' id ' } } ) ... | if arg is None :
arg = [ ]
try :
arg = dict ( arg )
except ValueError :
arg = dict . fromkeys ( list ( arg ) , { } )
return arg |
def to_practice_counts ( request ) :
"""Get number of items available to practice .
filters : - - use this or body
json as in BODY
language :
language of the items
BODY
json in following format :
" # identifier " : [ ] - - custom identifier ( str ) and filter""" | data = None
if request . method == "POST" :
data = json . loads ( request . body . decode ( "utf-8" ) ) [ "filters" ]
if "filters" in request . GET :
data = load_query_json ( request . GET , "filters" )
if data is None or len ( data ) == 0 :
return render_json ( request , { } , template = 'models_json.html'... |
def _load_data ( self , reset = False ) :
'''loads the RDF / turtle application data to the triplestore
args :
reset ( bool ) : True will delete the definition dataset and reload
all of the datafiles .''' | log = logging . getLogger ( "%s.%s" % ( self . log_name , inspect . stack ( ) [ 0 ] [ 3 ] ) )
log . setLevel ( self . log_level )
for attr , obj in self . datafile_obj . items ( ) :
if reset or obj [ 'latest_mod' ] > obj [ 'last_json_mod' ] :
conn = obj [ 'conn' ]
sparql = "DROP ALL;"
if os ... |
def listen ( self ) :
"""Listen for incoming control messages .
If the ' redis . shard _ hint ' configuration is set , its value will
be passed to the pubsub ( ) method when setting up the
subscription . The control channel to subscribe to is
specified by the ' redis . control _ channel ' configuration
( ... | # Use a specific database handle , with override . This allows
# the long - lived listen thread to be configured to use a
# different database or different database options .
db = self . config . get_database ( 'control' )
# Need a pub - sub object
kwargs = { }
if 'shard_hint' in self . config [ 'control' ] :
kwarg... |
def aggregated_relevant_items ( raw_df ) :
"""Aggragation for calculate mean and std .""" | df = ( raw_df [ [ 'idSegmento' , 'idPlanilhaItens' , 'VlUnitarioAprovado' ] ] . groupby ( by = [ 'idSegmento' , 'idPlanilhaItens' ] ) . agg ( [ np . mean , lambda x : np . std ( x , ddof = 0 ) ] ) )
df . columns = df . columns . droplevel ( 0 )
return ( df . rename ( columns = { '<lambda>' : 'std' } ) ) |
def login_required ( fn ) :
"""Decorator that restrict access only for authorized users .
User is considered authorized if authorized _ userid
returns some value .""" | @ wraps ( fn )
async def wrapped ( * args , ** kwargs ) :
request = args [ - 1 ]
if not isinstance ( request , web . BaseRequest ) :
msg = ( "Incorrect decorator usage. " "Expecting `def handler(request)` " "or `def handler(self, request)`." )
raise RuntimeError ( msg )
await check_authorize... |
def find ( name ) :
"""Locate a filename into the shader library .""" | if op . exists ( name ) :
return name
path = op . dirname ( __file__ ) or '.'
paths = [ path ] + config [ 'include_path' ]
for path in paths :
filename = op . abspath ( op . join ( path , name ) )
if op . exists ( filename ) :
return filename
for d in os . listdir ( path ) :
fullpath = o... |
def remove_lvm_physical_volume ( block_device ) :
'''Remove LVM PV signatures from a given block device .
: param block _ device : str : Full path of block device to scrub .''' | p = Popen ( [ 'pvremove' , '-ff' , block_device ] , stdin = PIPE )
p . communicate ( input = 'y\n' ) |
def ParseURIFromKeyValues ( self , data , separator , uri_key ) :
"""Parse key / value formatted source listing and return potential URLs .
The fundamental shape of this format is as follows :
key : value # here : = separator
key : value
URI : [ URL ] # here URI = uri _ key
[ URL ] # this is where it beco... | precondition . AssertType ( data , Text )
precondition . AssertType ( separator , Text )
kv_entries = KeyValueParser ( kv_sep = separator ) . ParseEntries ( data )
spaced_entries = FieldParser ( ) . ParseEntries ( data )
uris = [ ]
check_uri_on_next_line = False
for kv_entry , sp_entry in zip ( kv_entries , spaced_entr... |
def head ( self , bytes ) :
"""Returns the number of given bytes from the head of the buffer .
The buffer remains unchanged .
: type bytes : int
: param bytes : The number of bytes to return .""" | oldpos = self . io . tell ( )
self . io . seek ( 0 )
head = self . io . read ( bytes )
self . io . seek ( oldpos )
return head |
def get_usedby_aql ( self , params ) :
"""Возвращает запрос AQL ( без репозитория ) , из файла конфигурации
: param params :
: return :""" | if self . _usedby is None :
return None
_result = { }
params = self . merge_valued ( params )
for k , v in self . _usedby [ 'AQL' ] . items ( ) :
if isinstance ( v , str ) :
k = k . format ( ** params )
v = v . format ( ** params )
_result [ k ] = v
return _result |
def random ( length , chars = None ) :
"""Generates a random string .
: param length : Length of the string to generate .
This can be a numbe or a pair : ` ` ( min _ length , max _ length ) ` `
: param chars : String of characters to choose from""" | if chars is None :
chars = string . ascii_letters + string . digits
else :
ensure_string ( chars )
if not chars :
raise ValueError ( "character set must not be empty" )
if is_pair ( length ) :
length = randint ( * length )
elif isinstance ( length , Integral ) :
if not length > 0 :
r... |
def mel ( sr , n_dft , n_mels = 128 , fmin = 0.0 , fmax = None , htk = False , norm = 1 ) :
"""[ np ] create a filterbank matrix to combine stft bins into mel - frequency bins
use Slaney ( said Librosa )
n _ mels : numbre of mel bands
fmin : lowest frequency [ Hz ]
fmax : highest frequency [ Hz ]
If ` Non... | return librosa . filters . mel ( sr = sr , n_fft = n_dft , n_mels = n_mels , fmin = fmin , fmax = fmax , htk = htk , norm = norm ) . astype ( K . floatx ( ) ) |
def upload_and_confirm ( self , incoming , ** kwargs ) :
"""Upload the file to okcupid and confirm , among other things , its
thumbnail position .
: param incoming : A filepath string , : class : ` . Info ` object or
a file like object to upload to okcupid . com .
If an info object is provided , its thumbna... | response_dict = self . upload ( incoming )
if 'error' in response_dict :
log . warning ( 'Failed to upload photo' )
return response_dict
if isinstance ( incoming , Info ) :
kwargs . setdefault ( 'thumb_nail_left' , incoming . thumb_nail_left )
kwargs . setdefault ( 'thumb_nail_top' , incoming . thumb_na... |
def service ( self , block , service_name ) :
"""Return a service , or None .
Services are objects implementing arbitrary other interfaces . They are
requested by agreed - upon names , see [ XXX TODO ] for a list of possible
services . The object returned depends on the service requested .
XBlocks must anno... | declaration = block . service_declaration ( service_name )
if declaration is None :
raise NoSuchServiceError ( "Service {!r} was not requested." . format ( service_name ) )
service = self . _services . get ( service_name )
if service is None and declaration == "need" :
raise NoSuchServiceError ( "Service {!r} i... |
def lock ( instance_id , profile = None , ** kwargs ) :
'''Lock an instance
instance _ id
ID of the instance to be locked
CLI Example :
. . code - block : : bash
salt ' * ' nova . lock 1138''' | conn = _auth ( profile , ** kwargs )
return conn . lock ( instance_id ) |
def get ( self , host , files_count , path = "/" , ssl = False , external = None ) :
"""Send get request to a url and wrap the results
: param host ( str ) : the host name of the url
: param path ( str ) : the path of the url ( start with " / " )
: return ( dict ) : the result of the test url""" | theme = "https" if ssl else "http"
url = host + path
http_url = theme + "://" + url
result = { }
try :
capture_path = os . getcwd ( ) + '/'
har_file_path = capture_path + "har/"
# fc . load _ page ( self . driver , http _ url )
fc . switch_tab ( self . driver )
self . load_page ( http_url )
prin... |
def get ( self , key , default_val = None , require_value = False ) :
"""Returns a dictionary value""" | val = dict . get ( self , key , default_val )
if val is None and require_value :
raise KeyError ( 'key "%s" not found' % key )
if isinstance ( val , dict ) :
return AttributeDict ( val )
return val |
def create_vmfs_datastore ( datastore_name , disk_id , vmfs_major_version , safety_checks = True , service_instance = None ) :
'''Creates a ESXi host disk group with the specified cache and capacity disks .
datastore _ name
The name of the datastore to be created .
disk _ id
The disk id ( canonical name ) o... | log . debug ( 'Validating vmfs datastore input' )
schema = VmfsDatastoreSchema . serialize ( )
try :
jsonschema . validate ( { 'datastore' : { 'name' : datastore_name , 'backing_disk_id' : disk_id , 'vmfs_version' : vmfs_major_version } } , schema )
except jsonschema . exceptions . ValidationError as exc :
rais... |
def remove_raw ( self , length_tag , value_tag ) :
"""Remove the tags for a data type field .
: param length _ tag : tag number of the length field .
: param value _ tag : tag number of the value field .
You can remove either private or standard data field definitions in
case a particular application uses t... | self . raw_len_tags . remove ( length_tag )
self . raw_data_tags . remove ( value_tag )
return |
def sign ( message , ** config ) :
"""Insert two new fields into the message dict and return it .
Those fields are :
- ' signature ' - the computed message digest of the JSON repr .
- ' certificate ' - the base64 certificate or gpg key of the signator .""" | if not _implementation :
init ( ** config )
return _implementation . sign ( message , ** config ) |
def _getSyntaxByLanguageName ( self , syntaxName ) :
"""Get syntax by its name . Name is defined in the xml file""" | xmlFileName = self . _syntaxNameToXmlFileName [ syntaxName ]
return self . _getSyntaxByXmlFileName ( xmlFileName ) |
def _val_pt_xml ( self ) :
"""The unicode XML snippet containing the ` ` < c : pt > ` ` elements containing
the values for this series .""" | xml = ''
for idx , value in enumerate ( self . _series . values ) :
if value is None :
continue
xml += ( ' <c:pt idx="{val_idx:d}">\n' ' <c:v>{value}</c:v>\n' ' </c:pt>\n' ) . format ( ** { 'val_idx' : idx , 'value' : value , } )
return xml |
def as_dictionary ( self ) :
"""Return the condition as a dictionary .
: return : dict""" | condition_dict = { "name" : self . name , "timelock" : self . timelock , "timeout" : self . timeout , "contractName" : self . contract_name , "functionName" : self . function_name , "events" : [ e . as_dictionary ( ) for e in self . events ] , "parameters" : [ p . as_dictionary ( ) for p in self . parameters ] , }
retu... |
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