signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def remove_node ( node_id = str , force = bool ) :
'''Remove a node from a swarm and the target needs to be a swarm manager
node _ id
The node id from the return of swarm . node _ ls
force
Forcefully remove the node / minion from the service
CLI Example :
. . code - block : : bash
salt ' * ' swarm . r... | client = docker . APIClient ( base_url = 'unix://var/run/docker.sock' )
try :
if force == 'True' :
service = client . remove_node ( node_id , force = True )
return service
else :
service = client . remove_node ( node_id , force = False )
return service
except TypeError :
salt... |
def logoff ( self ) :
"""Send a logoff request .
: rtype : bool""" | self . send ( C1218LogoffRequest ( ) )
data = self . recv ( )
if data == b'\x00' :
self . _initialized = False
return True
return False |
def change_site ( self , new_name , new_location = None , new_er_data = None , new_pmag_data = None , replace_data = False ) :
"""Update a site ' s name , location , er _ data , and pmag _ data .
By default , new data will be added in to pre - existing data , overwriting existing values .
If replace _ data is T... | self . name = new_name
if new_location :
self . location = new_location
self . update_data ( new_er_data , new_pmag_data , replace_data ) |
def gpu_iuwt_recomposition ( in1 , scale_adjust , store_on_gpu , smoothed_array ) :
"""This function calls the a trous algorithm code to recompose the input into a single array . This is the
implementation of the isotropic undecimated wavelet transform recomposition for a GPU .
INPUTS :
in1 ( no default ) : A... | wavelet_filter = ( 1. / 16 ) * np . array ( [ 1 , 4 , 6 , 4 , 1 ] , dtype = np . float32 )
# Filter - bank for use in the a trous algorithm .
wavelet_filter = gpuarray . to_gpu_async ( wavelet_filter )
# Determines scale with adjustment and creates a zero array on the GPU to store the output , unless smoothed _ array
#... |
def get_agent_sock_path ( env = None , sp = subprocess ) :
"""Parse gpgconf output to find out GPG agent UNIX socket path .""" | args = [ util . which ( 'gpgconf' ) , '--list-dirs' ]
output = check_output ( args = args , env = env , sp = sp )
lines = output . strip ( ) . split ( b'\n' )
dirs = dict ( line . split ( b':' , 1 ) for line in lines )
log . debug ( '%s: %s' , args , dirs )
return dirs [ b'agent-socket' ] |
def purge_archives ( self ) :
"""Delete older archived items .
Use the class attribute NUM _ KEEP _ ARCHIVED to control
how many items are kept .""" | klass = self . get_version_class ( )
qs = klass . normal . filter ( object_id = self . object_id , state = self . ARCHIVED ) . order_by ( '-last_save' ) [ self . NUM_KEEP_ARCHIVED : ]
for obj in qs :
obj . _delete_reverses ( )
klass . normal . filter ( vid = obj . vid ) . delete ( ) |
def save ( self ) :
"""Called by the parent settings dialog when the user clicks on the Save button .
Stores the current settings in the ConfigManager .""" | logger . debug ( "User requested to save settings. New settings: " + self . _settings_str ( ) )
cm . ConfigManager . SETTINGS [ cm . PROMPT_TO_SAVE ] = not self . autosave_checkbox . isChecked ( )
cm . ConfigManager . SETTINGS [ cm . SHOW_TRAY_ICON ] = self . show_tray_checkbox . isChecked ( )
# cm . ConfigManager . SE... |
def buffer ( self , geometries , inSR , distances , units , outSR = None , bufferSR = None , unionResults = True , geodesic = True ) :
"""The buffer operation is performed on a geometry service resource
The result of this operation is buffered polygons at the
specified distances for the input geometry array . O... | url = self . _url + "/buffer"
params = { "f" : "json" , "inSR" : inSR , "geodesic" : geodesic , "unionResults" : unionResults }
if isinstance ( geometries , list ) and len ( geometries ) > 0 :
g = geometries [ 0 ]
if isinstance ( g , Polygon ) :
params [ 'geometries' ] = { "geometryType" : "esriGeometry... |
def format_item ( format_spec , item , defaults = None ) :
"""Format an item according to the given output format .
The format can be gioven as either an interpolation string ,
or a Tempita template ( which has to start with " E { lb } E { lb } " ) ,
@ param format _ spec : The output format .
@ param item ... | template_engine = getattr ( format_spec , "__engine__" , None )
# TODO : Make differences between engines transparent
if template_engine == "tempita" or ( not template_engine and format_spec . startswith ( "{{" ) ) : # Set item , or field names for column titles
namespace = dict ( headers = not bool ( item ) )
... |
def traverseItems ( self , mode = TraverseMode . DepthFirst , parent = None ) :
"""Generates a tree iterator that will traverse the items of this tree
in either a depth - first or breadth - first fashion .
: param mode | < XTreeWidget . TraverseMode >
recurse | < bool >
: return < generator >""" | try :
if parent :
count = parent . childCount ( )
func = parent . child
else :
count = self . topLevelItemCount ( )
func = self . topLevelItem
except RuntimeError : # can be raised when iterating on a deleted tree widget .
return
next = [ ]
for i in range ( count ) :
try ... |
def musixmatch ( song ) :
"""Returns the lyrics found in musixmatch for the specified mp3 file or an
empty string if not found .""" | escape = re . sub ( "'-¡¿" , '' , URLESCAPE )
translate = { escape : '' , ' ' : '-' }
artist = song . artist . title ( )
artist = re . sub ( r"( '|' )" , '' , artist )
artist = re . sub ( r"'" , '-' , artist )
title = song . title
title = re . sub ( r"( '|' )" , '' , title )
title = re . sub ( r"'" , '-' , title )
arti... |
def _compress ( self , data , operation ) :
"""This private method compresses some data in a given mode . This is used
because almost all of the code uses the exact same setup . It wouldn ' t
have to , but it doesn ' t hurt at all .""" | # The ' algorithm ' for working out how big to make this buffer is from
# the Brotli source code , brotlimodule . cc .
original_output_size = int ( math . ceil ( len ( data ) + ( len ( data ) >> 2 ) + 10240 ) )
available_out = ffi . new ( "size_t *" )
available_out [ 0 ] = original_output_size
output_buffer = ffi . new... |
def split_sources ( srcs ) :
""": param srcs : sources
: returns : a pair ( split sources , split time ) or just the split _ sources""" | from openquake . hazardlib . source import splittable
sources = [ ]
split_time = { }
# src . id - > time
for src in srcs :
t0 = time . time ( )
mag_a , mag_b = src . get_min_max_mag ( )
min_mag = src . min_mag
if mag_b < min_mag : # discard the source completely
continue
has_serial = hasattr... |
def has_equal_value ( state , ordered = False , ndigits = None , incorrect_msg = None ) :
"""Verify if a student and solution query result match up .
This function must always be used after ' zooming ' in on certain columns or records ( check _ column , check _ row or check _ result ) .
` ` has _ equal _ value ... | if not hasattr ( state , "parent" ) :
raise ValueError ( "You can only use has_equal_value() on the state resulting from check_column, check_row or check_result." )
if incorrect_msg is None :
incorrect_msg = "Column `{{col}}` seems to be incorrect.{{' Make sure you arranged the rows correctly.' if ordered else ... |
def get_fieldsets ( self , request , obj = None ) :
"""Add fieldsets of placeholders to the list of already
existing fieldsets .""" | # some ugly business to remove freeze _ date
# from the field list
general_module = { 'fields' : list ( self . general_fields ) , 'classes' : ( 'module-general' , ) , }
default_fieldsets = list ( self . fieldsets )
if not request . user . has_perm ( 'pages.can_freeze' ) :
general_module [ 'fields' ] . remove ( 'fre... |
def create_zip_dir ( zipfile_path , * file_list ) :
"""This function creates a zipfile located in zipFilePath with the files in
the file list
# fileList can be both a comma separated list or an array""" | try :
if isinstance ( file_list , ( list , tuple ) ) : # unfolding list of list or tuple
if len ( file_list ) == 1 :
if isinstance ( file_list [ 0 ] , ( list , tuple ) ) :
file_list = file_list [ 0 ]
# converting string to iterable list
if isinstance ( file_list , str ) :... |
def _handle_skip_feature ( self , test_dict ) :
"""handle skip feature for test
- skip : skip current test unconditionally
- skipIf : skip current test if condition is true
- skipUnless : skip current test unless condition is true
Args :
test _ dict ( dict ) : test info
Raises :
SkipTest : skip test""... | # TODO : move skip to initialize
skip_reason = None
if "skip" in test_dict :
skip_reason = test_dict [ "skip" ]
elif "skipIf" in test_dict :
skip_if_condition = test_dict [ "skipIf" ]
if self . session_context . eval_content ( skip_if_condition ) :
skip_reason = "{} evaluate to True" . format ( skip... |
def append ( self , func , * args , ** kwargs ) :
"""add a task to the chain
takes the same parameters as async _ task ( )""" | self . chain . append ( ( func , args , kwargs ) )
# remove existing results
if self . started :
delete_group ( self . group )
self . started = False
return self . length ( ) |
def del_doc ( self , doc ) :
"""Delete a document""" | if not self . index_writer :
self . index_writer = self . index . writer ( )
if not self . label_guesser_updater :
self . label_guesser_updater = self . label_guesser . get_updater ( )
logger . info ( "Removing doc from the index: %s" % doc )
if doc . docid in self . _docs_by_id :
self . _docs_by_id . pop (... |
def decode_run_length ( run_length_list ) :
"""Function to decode a given list encoded with run - length encoding .
Here run - length encoding means : [ N , E ] represents N occurrences of element E .
If an element is not in such run - length format , it means this element appears once .
Examples :
decode _... | decoded_list = [ ]
for element in run_length_list :
if type ( element ) is list :
decoded_list . extend ( [ element [ 1 ] ] * element [ 0 ] )
else :
decoded_list . append ( element )
return decoded_list |
def __directory_list_descriptor ( self , configs ) :
"""Builds a directory list for an API .
Args :
configs : List of dicts containing the service configurations to list .
Returns :
A dictionary that can be deserialized into JSON in discovery list format .
Raises :
ApiConfigurationError : If there ' s s... | descriptor = { 'kind' : 'discovery#directoryList' , 'discoveryVersion' : 'v1' , }
items = [ ]
for config in configs :
item_descriptor = self . __item_descriptor ( config )
if item_descriptor :
items . append ( item_descriptor )
if items :
descriptor [ 'items' ] = items
return descriptor |
def get ( self , section , option , * args ) :
"""Get option value from section . If an option is secure ,
populates the plain text .""" | if self . is_secure_option ( section , option ) and self . keyring_available :
s_option = "%s%s" % ( section , option )
if self . _unsaved . get ( s_option , [ '' ] ) [ 0 ] == 'set' :
res = self . _unsaved [ s_option ] [ 1 ]
else :
res = keyring . get_password ( self . keyring_name , s_optio... |
def raw_order_book ( self , pair , prec = None , ** kwargs ) :
"""Subscribe to the passed pair ' s raw order book channel .
: param pair : str , Pair to request data for .
: param kwargs :
: return :""" | prec = 'R0' if prec is None else prec
self . _subscribe ( 'book' , pair = pair , prec = prec , ** kwargs ) |
def windchill ( temperature , speed , face_level_winds = False , mask_undefined = True ) :
r"""Calculate the Wind Chill Temperature Index ( WCTI ) .
Calculates WCTI from the current temperature and wind speed using the formula
outlined by the FCM [ FCMR192003 ] _ .
Specifically , these formulas assume that wi... | # Correct for lower height measurement of winds if necessary
if face_level_winds : # No in - place so that we copy
# noinspection PyAugmentAssignment
speed = speed * 1.5
temp_limit , speed_limit = 10. * units . degC , 3 * units . mph
speed_factor = speed . to ( 'km/hr' ) . magnitude ** 0.16
wcti = units . Quantity ... |
def ext_pillar ( minion_id , pillar , # pylint : disable = W0613
use_grain = False , minion_ids = None , tag_match_key = None , tag_match_value = 'asis' , tag_list_key = None , tag_list_sep = ';' ) :
'''Execute a command and read the output as YAML''' | valid_tag_match_value = [ 'uqdn' , 'asis' ]
# meta - data : instance - id
grain_instance_id = __grains__ . get ( 'meta-data' , { } ) . get ( 'instance-id' , None )
if not grain_instance_id : # dynamic : instance - identity : document : instanceId
grain_instance_id = __grains__ . get ( 'dynamic' , { } ) . get ( 'ins... |
def follow_link ( self , link = None , * args , ** kwargs ) :
"""Follow a link .
If ` ` link ` ` is a bs4 . element . Tag ( i . e . from a previous call to
: func : ` links ` or : func : ` find _ link ` ) , then follow the link .
If ` ` link ` ` doesn ' t have a * href * - attribute or is None , treat
` ` l... | link = self . _find_link_internal ( link , args , kwargs )
referer = self . get_url ( )
headers = { 'Referer' : referer } if referer else None
return self . open_relative ( link [ 'href' ] , headers = headers ) |
def SetSerializersProfiler ( self , serializers_profiler ) :
"""Sets the serializers profiler .
Args :
serializers _ profiler ( SerializersProfiler ) : serializers profiler .""" | self . _serializers_profiler = serializers_profiler
if self . _storage_file :
self . _storage_file . SetSerializersProfiler ( serializers_profiler ) |
def _nextNonSpaceColumn ( block , column ) :
"""Returns the column with a non - whitespace characters
starting at the given cursor position and searching forwards .""" | textAfter = block . text ( ) [ column : ]
if textAfter . strip ( ) :
spaceLen = len ( textAfter ) - len ( textAfter . lstrip ( ) )
return column + spaceLen
else :
return - 1 |
def get_network ( families = [ socket . AF_INET ] ) :
"""# > > > from psutil . _ common import snic
> > > import mock
> > > from collections import namedtuple
> > > snic = namedtuple ( ' snic ' , [ ' family ' , ' address ' , ' netmask ' , ' broadcast ' , ' ptp ' ] )
> > > MOCK = {
. . . " awdl0 " : [ snic... | nic = psutil . net_if_addrs ( )
ips = defaultdict ( list )
# return nic
for card , addresses in nic . items ( ) :
for address in addresses :
if address . family in families :
ips [ card ] . append ( "{0.address}/{0.netmask}" . format ( address ) )
return dict ( ips ) |
def sample ( self , n ) :
"""Samples data into a Pandas DataFrame . Note that it calls BigQuery so it will
incur cost .
Args :
n : number of sampled counts . Note that the number of counts returned is approximated .
Returns :
A dataframe containing sampled data .
Raises :
Exception if n is larger than... | total = bq . Query ( 'select count(*) from %s' % self . _get_source ( ) ) . execute ( ) . result ( ) [ 0 ] . values ( ) [ 0 ]
if n > total :
raise ValueError ( 'sample larger than population' )
sampling = bq . Sampling . random ( percent = n * 100.0 / float ( total ) )
if self . _query is not None :
source = se... |
def select_tag ( self , uid ) :
"""Selects tag for further usage .
uid - - list or tuple with four bytes tag ID
Returns error state .""" | back_data = [ ]
buf = [ ]
buf . append ( self . act_select )
buf . append ( 0x70 )
for i in range ( 5 ) :
buf . append ( uid [ i ] )
crc = self . calculate_crc ( buf )
buf . append ( crc [ 0 ] )
buf . append ( crc [ 1 ] )
( error , back_data , back_length ) = self . card_write ( self . mode_transrec , buf )
if ( no... |
def _inserts ( self ) :
"""thwe""" | return { concat ( a , c , b ) for a , b in self . slices for c in ALPHABET } |
def send ( self , message , callback , timeout = 0 ) :
"""Add a single message to the internal pending queue to be processed
by the Connection without waiting for it to be sent .
: param message : The message to send .
: type message : ~ uamqp . message . Message
: param callback : The callback to be run on... | # pylint : disable = protected - access
try :
raise self . _error
except TypeError :
pass
except Exception as e :
_logger . warning ( "%r" , e )
raise
c_message = message . get_message ( )
message . _on_message_sent = callback
try :
self . _session . _connection . lock ( timeout = - 1 )
return s... |
def dump2sqlite ( records , output_file ) :
"""Dumps tests results to database .""" | results_keys = list ( records . results [ 0 ] . keys ( ) )
pad_data = [ ]
for key in REQUIRED_KEYS :
if key not in results_keys :
results_keys . append ( key )
pad_data . append ( "" )
conn = sqlite3 . connect ( os . path . expanduser ( output_file ) , detect_types = sqlite3 . PARSE_DECLTYPES )
# in... |
def set_dhw_on ( self , until = None ) :
"""Sets the DHW on until a given time , or permanently .""" | if until is None :
data = { "Mode" : "PermanentOverride" , "State" : "On" , "UntilTime" : None }
else :
data = { "Mode" : "TemporaryOverride" , "State" : "On" , "UntilTime" : until . strftime ( '%Y-%m-%dT%H:%M:%SZ' ) }
self . _set_dhw ( data ) |
def isDocumentCollection ( cls , name ) :
"""return true or false wether ' name ' is the name of a document collection .""" | try :
col = cls . getCollectionClass ( name )
return issubclass ( col , Collection )
except KeyError :
return False |
def conv3x3 ( in_planes , out_planes , stride = 1 ) :
"3x3 convolution with padding" | return nn . Conv2d ( in_planes , out_planes , kernel_size = 3 , stride = stride , padding = 1 , bias = True ) |
def sparse_decom2 ( inmatrix , inmask = ( None , None ) , sparseness = ( 0.01 , 0.01 ) , nvecs = 3 , its = 20 , cthresh = ( 0 , 0 ) , statdir = None , perms = 0 , uselong = 0 , z = 0 , smooth = 0 , robust = 0 , mycoption = 0 , initialization_list = [ ] , initialization_list2 = [ ] , ell1 = 10 , prior_weight = 0 , verbo... | if inmatrix [ 0 ] . shape [ 0 ] != inmatrix [ 1 ] . shape [ 0 ] :
raise ValueError ( 'Matrices must have same number of rows (samples)' )
idim = 3
if isinstance ( inmask [ 0 ] , iio . ANTsImage ) :
maskx = inmask [ 0 ] . clone ( 'float' )
idim = inmask [ 0 ] . dimension
hasmaskx = 1
elif isinstance ( in... |
def allow_exception ( self , exc_class ) :
"""Allow raising this class of exceptions from commands .
When a command fails on the server side due to an exception , by
default it is turned into a string and raised on the client side as an
ExternalError . The original class name is sent but ignored . If you
wo... | name = exc_class . __name__
self . _allowed_exceptions [ name ] = exc_class |
def rotation_substring_check ( main_string , check_string ) :
"""Checks if check _ string or any of its rotations is a substring of main _ string .
Returns True if it is , False otherwise .
Args :
main _ string ( str ) : The main string in which to check for substrings .
check _ string ( str ) : The string ... | check_length = len ( check_string )
double_check_string = check_string + check_string
for index in range ( len ( main_string ) - check_length + 1 ) :
for subset_index in range ( check_length + 1 ) :
if main_string [ index : index + check_length ] == double_check_string [ subset_index : subset_index + check_... |
def _next_sample_index ( self ) :
"""StochasticMux chooses its next sample stream randomly""" | return self . rng . choice ( self . n_active , p = ( self . stream_weights_ / self . weight_norm_ ) ) |
async def datacenters ( self ) :
"""Queries for WAN coordinates of Consul servers
Returns :
Mapping : WAN network coordinates for all Consul
servers , organized by DCs .
It returns a body like this : :
" dc1 " : {
" Datacenter " : " dc1 " ,
" Coordinates " : [
" Node " : " agent - one " ,
" Coord ... | response = await self . _api . get ( "/v1/coordinate/datacenters" )
return { data [ "Datacenter" ] : data for data in response . body } |
def rex ( expr ) :
"""Regular expression matcher to use together with transform functions""" | r = re . compile ( expr )
return lambda key : isinstance ( key , six . string_types ) and r . match ( key ) |
def rename ( self , node ) :
"""Translate a rename node into latex qtree node .
: param node : a treebrd node
: return : a qtree subtree rooted at the node""" | child = self . translate ( node . child )
attributes = ''
if node . attributes :
attributes = '({})' . format ( ', ' . join ( node . attributes . names ) )
return '[.${op}_{{{name}{attributes}}}$ {child} ]' . format ( op = latex_operator [ node . operator ] , name = node . name , attributes = attributes , child = c... |
def create_notification ( self ) :
"""Instead of the typical create _ widget we use ` create _ notification `
because after it ' s closed it needs created again .""" | d = self . declaration
builder = self . builder = Notification . Builder ( self . get_context ( ) , d . channel_id )
d = self . declaration
# Apply any custom settings
if d . settings :
builder . update ( ** d . settings )
for k , v in self . get_declared_items ( ) :
handler = getattr ( self , 'set_{}' . format... |
def is_citeable ( publication_info ) :
"""Check some fields in order to define if the article is citeable .
: param publication _ info : publication _ info field
already populated
: type publication _ info : list""" | def _item_has_pub_info ( item ) :
return all ( key in item for key in ( 'journal_title' , 'journal_volume' ) )
def _item_has_page_or_artid ( item ) :
return any ( key in item for key in ( 'page_start' , 'artid' ) )
has_pub_info = any ( _item_has_pub_info ( item ) for item in publication_info )
has_page_or_artid... |
def parse_meta ( meta_str ) :
"""Parse the metadata for a single ds9 region string .
Parameters
meta _ str : ` str `
Meta string , the metadata is everything after the close - paren of the
region coordinate specification . All metadata is specified as
key = value pairs separated by whitespace , but someti... | keys_vals = [ ( x , y ) for x , _ , y in regex_meta . findall ( meta_str . strip ( ) ) ]
extra_text = regex_meta . split ( meta_str . strip ( ) ) [ - 1 ]
result = OrderedDict ( )
for key , val in keys_vals : # regex can include trailing whitespace or inverted commas
# remove it
val = val . strip ( ) . strip ( "'" )... |
def has_more_pages ( self ) :
""": return : ` ` True ` ` if there are more pages available on the server .""" | # if has _ next property exists , it represents whether more pages exist
if self . has_next is not None :
return self . has_next
# otherwise , try to compute whether or not more pages exist
total_pages = self . get_total_pages ( )
if self . page_number is None or total_pages is None :
return None
else :
ret... |
def render_stop_display ( step : 'projects.ProjectStep' , message : str ) :
"""Renders a stop action to the Cauldron display .""" | stack = render_stack . get_formatted_stack_frame ( project = step . project , error_stack = False )
try :
names = [ frame [ 'filename' ] for frame in stack ]
index = names . index ( os . path . realpath ( __file__ ) )
frame = stack [ index - 1 ]
except Exception :
frame = { }
stop_message = ( '{}' . for... |
def delete_namespaced_daemon_set ( self , name , namespace , ** kwargs ) : # noqa : E501
"""delete _ namespaced _ daemon _ set # noqa : E501
delete a DaemonSet # noqa : E501
This method makes a synchronous HTTP request by default . To make an
asynchronous HTTP request , please pass async _ req = True
> > > ... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'async_req' ) :
return self . delete_namespaced_daemon_set_with_http_info ( name , namespace , ** kwargs )
# noqa : E501
else :
( data ) = self . delete_namespaced_daemon_set_with_http_info ( name , namespace , ** kwargs )
# noqa : E501
re... |
def start ( self ) :
"""Start all the registered services .
A new container is created for each service using the container
class provided in the _ _ init _ _ method .
All containers are started concurrently and the method will block
until all have completed their startup routine .""" | service_names = ', ' . join ( self . service_names )
_log . info ( 'starting services: %s' , service_names )
SpawningProxy ( self . containers ) . start ( )
_log . debug ( 'services started: %s' , service_names ) |
def makedirs ( self ) :
"""Create all parent folders if they do not exist .""" | normpath = os . path . normpath ( self . path )
parentfolder = os . path . dirname ( normpath )
if parentfolder :
try :
os . makedirs ( parentfolder )
except OSError :
pass |
def Chisholm ( m , x , rhol , rhog , mul , mug , D , roughness = 0 , L = 1 , rough_correction = False ) :
r'''Calculates two - phase pressure drop with the Chisholm ( 1973 ) correlation
from [ 1 ] _ , also in [ 2 ] _ and [ 3 ] _ .
. . math : :
\ frac { \ Delta P _ { tp } } { \ Delta P _ { lo } } = \ phi _ { c... | G_tp = m / ( pi / 4 * D ** 2 )
n = 0.25
# Blasius friction factor exponent
# 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... |
def unique_hash ( filepath : str , blocksize : int = 80 ) -> str :
"""Small function to generate a hash to uniquely generate a file .
Default blocksize is ` 500 `""" | s = sha1 ( )
with open ( filepath , "rb" ) as f :
buf = f . read ( blocksize )
s . update ( buf )
return s . hexdigest ( ) |
def vasp_version_from_outcar ( filename = 'OUTCAR' ) :
"""Returns the first line from a VASP OUTCAR file , to get the VASP source version string .
Args :
filename ( Str , optional ) : OUTCAR filename . Defaults to ' OUTCAR ' .
Returns :
( Str ) : The first line read from the OUTCAR file .""" | with open ( filename ) as f :
line = f . readline ( ) . strip ( )
return line |
def get_hla ( sample , cromwell_dir , hla_glob ) :
"""Retrieve HLA calls and input fastqs for a sample .""" | hla_dir = glob . glob ( os . path . join ( cromwell_dir , hla_glob , "align" , sample , "hla" ) ) [ 0 ]
fastq = os . path . join ( hla_dir , "OptiType-HLA-A_B_C-input.fq" )
calls = os . path . join ( hla_dir , "%s-optitype.csv" % sample )
return fastq , calls |
def _optimal_size ( self , capacity , error ) :
"""Calculates minimum number of bits in filter array and
number of hash functions given a number of enteries ( maximum )
and the desired error rate ( falese positives ) .
Example :
m , k = self . _ optimal _ size ( 3000 , 0.01 ) # m = 28756 , k = 7""" | m = math . ceil ( ( capacity * math . log ( error ) ) / math . log ( 1.0 / ( math . pow ( 2.0 , math . log ( 2.0 ) ) ) ) )
k = math . ceil ( math . log ( 2.0 ) * m / capacity )
return int ( m ) , int ( k ) |
def get ( self , key , default = NoDefault ) :
"""Retrieve a value from its key .
Retrieval steps are :
1 ) Normalize the key
2 ) For each option group :
a ) Retrieve the value at that key
b ) If no value exists , continue
c ) If the value is an instance of ' Default ' , continue
d ) Otherwise , retur... | key = normalize_key ( key )
if default is NoDefault :
defaults = [ ]
else :
defaults = [ default ]
for options in self . options :
try :
value = options [ key ]
except KeyError :
continue
if isinstance ( value , Default ) :
defaults . append ( value . value )
continue... |
def execute ( ) :
"""Ensure provisioning""" | boto_server_error_retries = 3
# Ensure provisioning
for table_name , table_key in sorted ( dynamodb . get_tables_and_gsis ( ) ) :
try :
table_num_consec_read_checks = CHECK_STATUS [ 'tables' ] [ table_name ] [ 'reads' ]
except KeyError :
table_num_consec_read_checks = 0
try :
table_n... |
def run ( args ) :
"""Args :
args ( argparse . Namespace )""" | regex_extractor = RegexExtractor ( pattern = args . pattern )
with warnings . catch_warnings ( ) :
warnings . simplefilter ( 'ignore' )
for line in args . input_file :
extractions = regex_extractor . extract ( line )
for e in extractions :
print ( e . value ) |
def read_block_data ( self , i2c_addr , register , force = None ) :
"""Read a block of up to 32 - bytes from a given register .
: param i2c _ addr : i2c address
: type i2c _ addr : int
: param register : Start register
: type register : int
: param force :
: type force : Boolean
: return : List of byt... | self . _set_address ( i2c_addr , force = force )
msg = i2c_smbus_ioctl_data . create ( read_write = I2C_SMBUS_READ , command = register , size = I2C_SMBUS_BLOCK_DATA )
ioctl ( self . fd , I2C_SMBUS , msg )
length = msg . data . contents . block [ 0 ]
return msg . data . contents . block [ 1 : length + 1 ] |
def remove_from_organization ( self , delete_account = False ) :
"""Remove a user from the organization ' s list of visible users . Optionally also delete the account .
Deleting the account can only be done if the organization owns the account ' s domain .
: param delete _ account : Whether to delete the accoun... | self . append ( removeFromOrg = { "deleteAccount" : True if delete_account else False } )
return None |
def widont_html ( value ) :
"""Add an HTML non - breaking space between the final two words at the end of
( and in sentences just outside of ) block level tags to avoid " widowed "
words .
Examples :
> > > print ( widont _ html ( ' < h2 > Here is a simple example < / h2 > < p > Single < / p > ' ) )
< h2 >... | def replace ( matchobj ) :
return force_text ( '%s %s%s' % matchobj . groups ( ) )
return re_widont_html . sub ( replace , force_text ( value ) ) |
def normalize_total ( adata , target_sum = None , fraction = 1 , key_added = None , layers = None , layer_norm = None , inplace = True ) :
"""{ norm _ descr }
{ params _ bulk }
{ norm _ return }
{ examples }""" | if fraction < 0 or fraction > 1 :
raise ValueError ( 'Choose fraction between 0 and 1.' )
X = adata . X
gene_subset = None
if not inplace : # not recarray because need to support sparse
dat = { }
if fraction < 1 :
logg . msg ( 'normalizing by count per cell for \
genes that make up less th... |
def get_cell_dimensions ( self ) :
"""Calculate centroid , width , length and area of each mesh cell .
: returns :
Tuple of four elements , each being 2d numpy array .
Each array has both dimensions less by one the dimensions
of the mesh , since they represent cells , not vertices .
Arrays contain the fol... | points , along_azimuth , updip , diag = self . triangulate ( )
top = along_azimuth [ : - 1 ]
left = updip [ : , : - 1 ]
tl_area = geo_utils . triangle_area ( top , left , diag )
top_length = numpy . sqrt ( numpy . sum ( top * top , axis = - 1 ) )
left_length = numpy . sqrt ( numpy . sum ( left * left , axis = - 1 ) )
b... |
def _sub_ms_char ( self , match ) :
"""Changes a MS smart quote character to an XML or HTML
entity , or an ASCII character .""" | orig = match . group ( 1 )
if self . smart_quotes_to == 'ascii' :
sub = self . MS_CHARS_TO_ASCII . get ( orig ) . encode ( )
else :
sub = self . MS_CHARS . get ( orig )
if type ( sub ) == tuple :
if self . smart_quotes_to == 'xml' :
sub = '&#x' . encode ( ) + sub [ 1 ] . encode ( ) + ';'... |
def error_codes ( self ) :
"""ThreatConnect error codes .""" | if self . _error_codes is None :
from . tcex_error_codes import TcExErrorCodes
self . _error_codes = TcExErrorCodes ( )
return self . _error_codes |
def IntegerField ( default = NOTHING , required = True , repr = True , cmp = True , key = None ) :
"""Create new int field on a model .
: param default : any integer value
: param bool required : whether or not the object is invalid if not provided .
: param bool repr : include this field should appear in obj... | default = _init_fields . init_default ( required , default , None )
validator = _init_fields . init_validator ( required , int )
return attrib ( default = default , converter = converters . int_if_not_none , validator = validator , repr = repr , cmp = cmp , metadata = dict ( key = key ) ) |
def init_original_response ( self ) :
"""Get the original response for comparing , confirm ` ` is _ cookie _ necessary ` `""" | if 'json' in self . request :
self . request [ 'data' ] = json . dumps ( self . request . pop ( 'json' ) ) . encode ( self . encoding )
r1 = self . req . request ( retry = self . retry , timeout = self . timeout , ** self . request )
resp = r1 . x
assert resp , ValueError ( 'original_response should not be failed. ... |
def db990 ( self , value = None ) :
"""Corresponds to IDD Field ` db990 `
Dry - bulb temperature corresponding to 90.0 % annual cumulative
frequency of occurrence ( cold conditions )
Args :
value ( float ) : value for IDD Field ` db990 `
Unit : C
if ` value ` is None it will not be checked against the
... | if value is not None :
try :
value = float ( value )
except ValueError :
raise ValueError ( 'value {} need to be of type float ' 'for field `db990`' . format ( value ) )
self . _db990 = value |
def touch_tip ( self , location = None , radius = 1.0 , v_offset = - 1.0 , speed = 60.0 ) :
"""Touch the : any : ` Pipette ` tip to the sides of a well ,
with the intent of removing left - over droplets
Notes
If no ` location ` is passed , the pipette will touch _ tip
from it ' s current position .
Parame... | if not self . tip_attached :
log . warning ( "Cannot touch tip without a tip attached." )
if speed > 80.0 :
log . warning ( "Touch tip speeds greater than 80mm/s not allowed" )
speed = 80.0
if speed < 20.0 :
log . warning ( "Touch tip speeds greater than 80mm/s not allowed" )
speed = 20.0
if helpers... |
def mogrify ( self , query , args = None ) :
"""Returns the exact string that is sent to the database by calling
the execute ( ) method . This method follows the extension to the DB
API 2.0 followed by Psycopg .
: param query : ` ` str ` ` sql statement
: param args : ` ` tuple ` ` or ` ` list ` ` of argume... | conn = self . _get_db ( )
if args is not None :
query = query % self . _escape_args ( args , conn )
return query |
def palettize ( arr , colors , values ) :
"""From start * values * apply * colors * to * data * .""" | new_arr = np . digitize ( arr . ravel ( ) , np . concatenate ( ( values , [ max ( np . nanmax ( arr ) , values . max ( ) ) + 1 ] ) ) )
new_arr -= 1
new_arr = new_arr . clip ( min = 0 , max = len ( values ) - 1 )
try :
new_arr = np . ma . array ( new_arr . reshape ( arr . shape ) , mask = arr . mask )
except Attribu... |
def _grid_in_property ( field_name , docstring , read_only = False , closed_only = False ) :
"""Create a GridIn property .""" | def getter ( self ) :
if closed_only and not self . _closed :
raise AttributeError ( "can only get %r on a closed file" % field_name )
# Protect against PHP - 237
if field_name == 'length' :
return self . _file . get ( field_name , 0 )
return self . _file . get ( field_name , None )
def ... |
def depth_first_search ( graph , root_node = None ) :
"""Searches through the tree in a breadth - first fashion .
If root _ node is None , an arbitrary node will be used as the root .
If root _ node is not None , it will be used as the root for the search tree .
Returns a list of nodes , in the order that the... | ordering , parent_lookup , children_lookup = depth_first_search_with_parent_data ( graph , root_node )
return ordering |
def dot_product_self_attention_relative_v2 ( q , k , v , bias , max_relative_position = None , dropout_rate = 0.0 , image_shapes = None , name = None , make_image_summary = True , dropout_broadcast_dims = None , heads_share_relative_embedding = False , add_relative_to_values = False ) :
"""Calculate relative positi... | if not max_relative_position :
raise ValueError ( "Max relative position (%s) should be > 0 when using " "relative self attention." % ( max_relative_position ) )
with tf . variable_scope ( name , default_name = "dot_product_self_attention_relative_v2" , values = [ q , k , v ] ) : # This calculation only works for s... |
def append ( self , item ) :
"""Appends a ` Monomer to the ` Polymer ` .
Notes
Does not update labelling .""" | if isinstance ( item , Monomer ) :
self . _monomers . append ( item )
else :
raise TypeError ( 'Only Monomer objects can be appended to an Polymer.' )
return |
def serialize_unicode ( self , data ) :
"""Special handling for serializing unicode strings in Py2.
Encode to UTF - 8 if unicode , otherwise handle as a str .
: param data : Object to be serialized .
: rtype : str""" | try :
return data . value
except AttributeError :
pass
try :
if isinstance ( data , unicode ) :
return data . encode ( encoding = 'utf-8' )
except NameError :
return str ( data )
else :
return str ( data ) |
def client_for ( self , config_path , quiet = False , bootstrap_server = False , create_client = False ) :
"""Get a cached client for a project , otherwise create one .""" | client = None
abs_path = os . path . abspath ( config_path )
if abs_path in self . clients :
client = self . clients [ abs_path ]
elif create_client :
client = self . create_client ( config_path )
if client . setup ( quiet = quiet , bootstrap_server = bootstrap_server ) :
self . clients [ abs_path ]... |
def get ( self , * args , ** kwargs ) -> "QuerySet" :
"""Fetch exactly one object matching the parameters .""" | queryset = self . filter ( * args , ** kwargs )
queryset . _limit = 2
queryset . _get = True
return queryset |
def set_display_name ( self , display_name ) :
'''Set display name of a system independently of upload .''' | if self . config . legacy_upload :
return self . _legacy_set_display_name ( display_name )
system = self . _fetch_system_by_machine_id ( )
if not system :
return system
inventory_id = system [ 0 ] [ 'id' ]
req_url = self . base_url + '/inventory/v1/hosts/' + inventory_id
try :
net_logger . info ( "PATCH %s"... |
def global_state ( self ) :
"""Returns global variables for generating function from ` ` func _ code ` ` . Includes
compiled regular expressions and imports , so it does not have to do it every
time when validation function is called .""" | self . _generate_func_code ( )
return dict ( REGEX_PATTERNS = self . _compile_regexps , re = re , JsonSchemaException = JsonSchemaException , ) |
def start_search ( self ) :
"""Start the Gateway Search Request and return the address information
: rtype : ( string , int )
: return : a tuple ( string ( IP ) , int ( Port ) when found or None when
timeout occurs""" | self . _asyncio_loop = asyncio . get_event_loop ( )
# Creating Broadcast Receiver
coroutine_listen = self . _asyncio_loop . create_datagram_endpoint ( lambda : self . KNXSearchBroadcastReceiverProtocol ( self . _process_response , self . _timeout_handling , self . _timeout , self . _asyncio_loop ) , local_addr = ( self... |
def _clean_result ( self , text ) :
"""Remove double spaces , punctuation and escapes apostrophes .""" | text = re . sub ( '\s\s+' , ' ' , text )
text = re . sub ( '\.\.+' , '.' , text )
text = text . replace ( "'" , "\\'" )
return text |
def OnExport ( self , event ) :
"""File export event handler
Currently , only CSV export is supported""" | code_array = self . main_window . grid . code_array
tab = self . main_window . grid . current_table
selection = self . main_window . grid . selection
# Check if no selection is present
selection_bbox = selection . get_bbox ( )
f2w = get_filetypes2wildcards ( [ "csv" , "pdf" , "svg" ] )
filters = f2w . keys ( )
wildcard... |
def addAdminResource ( self , pluginSubPath : bytes , resource : BasicResource ) -> None :
"""Add Site Resource
Add a cusotom implementation of a served http resource .
: param pluginSubPath : The resource path where you want to serve this resource .
: param resource : The resource to serve .
: return : Non... | pluginSubPath = pluginSubPath . strip ( b'/' )
self . __rootAdminResource . putChild ( pluginSubPath , resource ) |
def convert_machine_list_time_val ( text : str ) -> datetime . datetime :
'''Convert RFC 3659 time - val to datetime objects .''' | # TODO : implement fractional seconds
text = text [ : 14 ]
if len ( text ) != 14 :
raise ValueError ( 'Time value not 14 chars' )
year = int ( text [ 0 : 4 ] )
month = int ( text [ 4 : 6 ] )
day = int ( text [ 6 : 8 ] )
hour = int ( text [ 8 : 10 ] )
minute = int ( text [ 10 : 12 ] )
second = int ( text [ 12 : 14 ]... |
def checkpoint_filepath ( checkpoint , pm ) :
"""Create filepath for indicated checkpoint .
: param str | pypiper . Stage checkpoint : Pipeline phase / stage or one ' s name
: param pypiper . PipelineManager | pypiper . Pipeline pm : manager of a pipeline
instance , relevant for output folder path .
: retur... | # Handle case in which checkpoint is given not just as a string , but
# as a checkpoint - like filename . Don ' t worry about absolute path status
# of a potential filename input , or whether it ' s in the pipeline ' s
# output folder . That ' s handled upstream . While this isn ' t a protected
# function , there ' s n... |
def actions_for_project ( self , project ) :
"""Compile & Run the experiment with - O3 enabled .""" | project . cflags = [ "-O3" , "-fno-omit-frame-pointer" ]
project . runtime_extension = time . RunWithTime ( run . RuntimeExtension ( project , self ) )
return self . default_runtime_actions ( project ) |
def tree_analysisOutput ( self , * args , ** kwargs ) :
"""An optional method for looping over the < outputTree > and
calling an outputcallback on the analysis results at each
path .
Only call this if self . b _ persisAnalysisResults is True .""" | fn_outputcallback = None
for k , v in kwargs . items ( ) :
if k == 'outputcallback' :
fn_outputcallback = v
index = 1
total = len ( self . d_inputTree . keys ( ) )
for path , d_analysis in self . d_outputTree . items ( ) :
self . simpleProgress_show ( index , total )
self . dp . qprint ( "Processing... |
def insert ( self , data ) :
"""Insert 1 into each bit by local _ hash""" | if not data :
return
data = self . _compress_by_md5 ( data )
# cut the first two place , route to different block by block _ num
name = self . key + str ( int ( data [ 0 : 2 ] , 16 ) % self . block_num )
for h in self . hash_function :
local_hash = h . hash ( data )
self . server . setbit ( name , local_has... |
def set_object ( cache , template , indexes , data ) :
"""Set an object in Redis using a pipeline .
Only sets the fields that are present in both the template and the data .
Arguments :
template : a dictionary containg the keys for the object and
template strings for the corresponding redis keys . The templ... | # TODO ( mattmillr ) : Handle expiration times
with cache as redis_connection :
pipe = redis_connection . pipeline ( )
for key in set ( template . keys ( ) ) & set ( data . keys ( ) ) :
pipe . set ( template [ key ] % indexes , str ( data [ key ] ) )
pipe . execute ( ) |
def upload_image ( self , image_file , referer_url = None , title = None , desc = None , created_at = None , collection_id = None ) :
"""Upload an image
: param image _ file : File - like object of an image file
: param referer _ url : Referer site URL
: param title : Site title
: param desc : Comment
: p... | url = self . upload_url + '/api/upload'
data = { }
if referer_url is not None :
data [ 'referer_url' ] = referer_url
if title is not None :
data [ 'title' ] = title
if desc is not None :
data [ 'desc' ] = desc
if created_at is not None :
data [ 'created_at' ] = str ( created_at )
if collection_id is not... |
def trim_tree_before ( element , include_element = True , keep_head = True ) :
"""Removes the document tree preceding the given element . If include _ element
is True , the given element is kept in the tree , otherwise it is removed .""" | el = element
for parent_el in element . iterancestors ( ) :
parent_el . text = None
if el != element or include_element :
el = el . getprevious ( )
else :
parent_el . text = el . tail
while el is not None :
remove_el = el
el = el . getprevious ( )
tag = remove_el ... |
def load_data ( train_path = './data/regression.train' , test_path = './data/regression.test' ) :
'''Load or create dataset''' | print ( 'Load data...' )
df_train = pd . read_csv ( train_path , header = None , sep = '\t' )
df_test = pd . read_csv ( test_path , header = None , sep = '\t' )
num = len ( df_train )
split_num = int ( 0.9 * num )
y_train = df_train [ 0 ] . values
y_test = df_test [ 0 ] . values
y_eval = y_train [ split_num : ]
y_train... |
def mkmanpage ( name ) :
"""Return man page content for the given ` cmdln . Cmdln ` subclass name .""" | mod_name , class_name = name . rsplit ( '.' , 1 )
mod = __import__ ( mod_name )
inst = getattr ( mod , class_name ) ( )
sections = cmdln . man_sections_from_cmdln ( inst )
sys . stdout . write ( '' . join ( sections ) ) |
def _is_subsequence_of ( self , sub , sup ) :
"""Parameters
sub : str
sup : str
Returns
bool""" | return bool ( re . search ( ".*" . join ( sub ) , sup ) ) |
def encode_index_req ( self , bucket , index , startkey , endkey = None , return_terms = None , max_results = None , continuation = None , timeout = None , term_regex = None , streaming = False ) :
"""Encodes a secondary index request into the protobuf message .
: param bucket : the bucket whose index to query
... | req = riak . pb . riak_kv_pb2 . RpbIndexReq ( bucket = str_to_bytes ( bucket . name ) , index = str_to_bytes ( index ) )
self . _add_bucket_type ( req , bucket . bucket_type )
if endkey is not None :
req . qtype = riak . pb . riak_kv_pb2 . RpbIndexReq . range
req . range_min = str_to_bytes ( str ( startkey ) )
... |
def crval ( self ) :
"""Get the world coordinate of the reference pixel .
@ rtype : float , float""" | try :
return self . wcs . crval1 , self . wcs . crval2
except Exception as ex :
logging . debug ( "Couldn't get CRVAL from WCS: {}" . format ( ex ) )
logging . debug ( "Trying RA/DEC values" )
try :
return ( float ( self [ 'RA-DEG' ] ) , float ( self [ 'DEC-DEG' ] ) )
except KeyError as ke :
KeyErro... |
def name ( self ) :
"""MessageHandler name .""" | return ffi . string ( lib . EnvGetDefmessageHandlerName ( self . _env , self . _cls , self . _idx ) ) . decode ( ) |
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