signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def get_associated_profile_names ( profile_path , result_role , org_vm , server , include_classnames = False ) :
"""Get the Associated profiles and return the string names ( org : name : version )
for each profile as a list .""" | insts = get_associated_profiles ( profile_path , result_role , server )
names = [ ]
for inst in insts :
if include_classnames :
names . append ( "(%s)%s" % ( inst . classname , profile_name ( org_vm , inst ) ) )
else :
names . append ( profile_name ( org_vm , inst ) )
return names |
def get_template_sources ( self , template_name , template_dirs = None ) :
"""Returns the absolute paths to " template _ name " in the specified app .
If the name does not contain an app name ( no colon ) , an empty list
is returned .
The parent FilesystemLoader . load _ template _ source ( ) will take care
... | if ':' not in template_name :
return [ ]
app_name , template_name = template_name . split ( ":" , 1 )
template_dir = get_app_template_dir ( app_name )
if template_dir :
try :
from django . template import Origin
origin = Origin ( name = join ( template_dir , template_name ) , template_name = tem... |
def transaction ( self , request ) :
"""Ideally at this method , you will check the
caller reference against a user id or uniquely
identifiable attribute ( if you are already not
using it as the caller reference ) and the type
of transaction ( either pay , reserve etc ) . For
the sake of the example , we ... | request_url = request . build_absolute_uri ( )
parsed_url = urlparse . urlparse ( request_url )
query = parsed_url . query
dd = dict ( map ( lambda x : x . split ( "=" ) , query . split ( "&" ) ) )
resp = self . purchase ( 100 , dd )
return HttpResponseRedirect ( "%s?status=%s" % ( reverse ( "app_offsite_amazon_fps" ) ... |
def pts_on_bezier_curve ( P = [ ( 0.0 , 0.0 ) ] , n_seg = 0 ) :
'''Return list N + 1 points representing N line segments on bezier curve
defined by control points P .''' | assert isinstance ( P , list )
assert len ( P ) > 0
for p in P :
assert isinstance ( p , tuple )
for i in p :
assert len ( p ) > 1
assert isinstance ( i , float )
assert isinstance ( n_seg , int )
assert n_seg >= 0
return [ pt_on_bezier_curve ( P , float ( i ) / n_seg ) for i in range ( n_seg ) ... |
def tempoAdjust2 ( self , tempoFactor ) :
"""Adjust tempo by aggregating active basal cell votes for pre vs . post
: param tempoFactor : scaling signal to MC clock from last sequence item
: return : adjusted scaling signal""" | late_votes = ( len ( self . adtm . getNextBasalPredictedCells ( ) ) - len ( self . apicalIntersect ) ) * - 1
early_votes = len ( self . apicalIntersect )
votes = late_votes + early_votes
print ( 'vote tally' , votes )
if votes > 0 :
tempoFactor = tempoFactor * 0.5
print 'speed up'
elif votes < 0 :
tempoFact... |
def get_raw ( self ) :
""": rtype : bytearray""" | buff = bytearray ( )
buff += writesleb128 ( self . size )
for i in self . handlers :
buff += i . get_raw ( )
if self . size <= 0 :
buff += writeuleb128 ( self . catch_all_addr )
return buff |
def saturation_equivalent_potential_temperature ( pressure , temperature ) :
r"""Calculate saturation equivalent potential temperature .
This calculation must be given an air parcel ' s pressure and temperature .
The implementation uses the formula outlined in [ Bolton1980 ] _ for the
equivalent potential tem... | t = temperature . to ( 'kelvin' ) . magnitude
p = pressure . to ( 'hPa' ) . magnitude
e = saturation_vapor_pressure ( temperature ) . to ( 'hPa' ) . magnitude
r = saturation_mixing_ratio ( pressure , temperature ) . magnitude
th_l = t * ( 1000 / ( p - e ) ) ** mpconsts . kappa
th_es = th_l * np . exp ( ( 3036. / t - 1.... |
def recognized_release ( self ) :
"""Check if this Release value is something we can parse .
: rtype : bool""" | _ , _ , rest = self . get_release_parts ( )
# If " rest " is not a well - known value here , then this package is
# using a Release value pattern we cannot recognize .
if rest == '' or re . match ( r'%{\??dist}' , rest ) :
return True
return False |
def load ( self ) :
"""Loads a user ' s inventory
Queries the user ' s inventory , parses each item , and adds
each item to the inventory . Note this class should not be
used directly , but rather usr . inventory should be used to
access a user ' s inventory .
Parameters
usr ( User ) - The user to load ... | self . items = { }
pg = self . usr . getPage ( "http://www.neopets.com/objects.phtml?type=inventory" )
# Indicates an empty inventory
if "You aren't carrying anything" in pg . content :
return
try :
for row in pg . find_all ( "td" , "contentModuleContent" ) [ 1 ] . table . find_all ( "tr" ) :
for item i... |
def copy ( self , other ) :
"""Copy metadata from another : py : class : ` Metadata ` object .
Returns the : py : class : ` Metadata ` object , allowing convenient
code like this : :
md = Metadata ( ) . copy ( other _ md )
: param Metadata other : The metadata to copy .
: rtype : : py : class : ` Metadata... | # copy from other to self
self . data . update ( other . data )
if other . comment is not None :
self . comment = other . comment
return self |
def get_reversed_statuses ( context ) :
"""Return a mapping of exit codes to status strings .
Args :
context ( scriptworker . context . Context ) : the scriptworker context
Returns :
dict : the mapping of exit codes to status strings .""" | _rev = { v : k for k , v in STATUSES . items ( ) }
_rev . update ( dict ( context . config [ 'reversed_statuses' ] ) )
return _rev |
def _incoming ( self , packet ) :
"""Callback for data received from the copter .""" | if len ( packet . data ) < 1 :
logger . warning ( 'Localization packet received with incorrect' + 'length (length is {})' . format ( len ( packet . data ) ) )
return
pk_type = struct . unpack ( '<B' , packet . data [ : 1 ] ) [ 0 ]
data = packet . data [ 1 : ]
# Decoding the known packet types
# TODO : more gene... |
def Description ( self ) :
"""Returns searchable data as Description""" | descr = " " . join ( ( self . getId ( ) , self . aq_parent . Title ( ) ) )
return safe_unicode ( descr ) . encode ( 'utf-8' ) |
def firstAnnot ( self ) :
"""Points to first annotation on page""" | CheckParent ( self )
val = _fitz . Page_firstAnnot ( self )
if val :
val . thisown = True
val . parent = weakref . proxy ( self )
# owning page object
self . _annot_refs [ id ( val ) ] = val
return val |
def resample ( old_wavelengths , new_wavelengths ) :
"""Resample a spectrum to a new wavelengths map while conserving total flux .
: param old _ wavelengths :
The original wavelengths array .
: type old _ wavelengths :
: class : ` numpy . array `
: param new _ wavelengths :
The new wavelengths array to ... | data = [ ]
old_px_indices = [ ]
new_px_indices = [ ]
for i , new_wl_i in enumerate ( new_wavelengths ) : # These indices should span just over the new wavelength pixel .
indices = np . unique ( np . clip ( old_wavelengths . searchsorted ( new_wavelengths [ i : i + 2 ] , side = "left" ) + [ - 1 , + 1 ] , 0 , old_wav... |
def update_ptr_record ( self , device , record , domain_name , data = None , ttl = None , comment = None ) :
"""Updates a PTR record with the supplied values .""" | device_type = self . _resolve_device_type ( device )
href , svc_name = self . _get_ptr_details ( device , device_type )
try :
rec_id = record . id
except AttributeError :
rec_id = record
rec = { "name" : domain_name , "id" : rec_id , "type" : "PTR" , "data" : data , }
if ttl is not None : # Minimum TTL is 300 s... |
def setArg ( self , namespace , key , value ) :
"""Set a single argument in this namespace""" | assert key is not None
assert value is not None
namespace = self . _fixNS ( namespace )
# try to ensure that internally it ' s consistent , at least : str - > str
if isinstance ( value , bytes ) :
value = str ( value , encoding = "utf-8" )
self . args [ ( namespace , key ) ] = value
if not ( namespace is BARE_NS ) ... |
def get_crystal_system ( self ) :
"""Get the crystal system for the structure , e . g . , ( triclinic ,
orthorhombic , cubic , etc . ) .
Returns :
( str ) : Crystal system for structure or None if system cannot be detected .""" | n = self . _space_group_data [ "number" ]
f = lambda i , j : i <= n <= j
cs = { "triclinic" : ( 1 , 2 ) , "monoclinic" : ( 3 , 15 ) , "orthorhombic" : ( 16 , 74 ) , "tetragonal" : ( 75 , 142 ) , "trigonal" : ( 143 , 167 ) , "hexagonal" : ( 168 , 194 ) , "cubic" : ( 195 , 230 ) }
crystal_sytem = None
for k , v in cs . i... |
def solve ( self ) :
"""Start ( or re - start ) optimisation . This method implements the
framework for the alternation between ` X ` and ` D ` updates in a
dictionary learning algorithm .
If option ` ` Verbose ` ` is ` ` True ` ` , the progress of the
optimisation is displayed at every iteration . At termi... | # Construct tuple of status display column titles and set status
# display strings
hdrtxt = [ 'Itn' , 'Fnc' , 'DFid' , u ( 'Regℓ1' ) ]
hdrstr , fmtstr , nsep = common . solve_status_str ( hdrtxt , fwdth0 = type ( self ) . fwiter , fprec = type ( self ) . fpothr )
# Print header and separator strings
if self . opt [ 'Ve... |
def stopThread ( self ) :
"""Stops spawned NSThread .""" | if self . _thread is not None :
self . performSelector_onThread_withObject_waitUntilDone_ ( 'stopPowerNotificationsThread' , self . _thread , None , objc . YES )
self . _thread = None |
def __getFormat ( self , format ) :
"""Defaults to JSON [ ps : ' RDF ' is the native rdflib representation ]""" | if format == "XML" :
self . sparql . setReturnFormat ( XML )
self . format = "XML"
elif format == "RDF" :
self . sparql . setReturnFormat ( RDF )
self . format = "RDF"
else :
self . sparql . setReturnFormat ( JSON )
self . format = "JSON" |
def init ( ) :
"""Execute init tasks for all components ( virtualenv , pip ) .""" | print ( yellow ( "# Setting up development environment...\n" , True ) )
virtualenv . init ( )
virtualenv . update ( )
print ( green ( "\n# DONE." , True ) )
print ( green ( "Type " ) + green ( "activate" , True ) + green ( " to enable your dev virtual environment." ) ) |
def maybe_sendraw ( self , host_port : Tuple [ int , int ] , messagedata : bytes ) :
"""Send message to recipient if the transport is running .""" | # Don ' t sleep if timeout is zero , otherwise a context - switch is done
# and the message is delayed , increasing its latency
sleep_timeout = self . throttle_policy . consume ( 1 )
if sleep_timeout :
gevent . sleep ( sleep_timeout )
# Check the udp socket is still available before trying to send the
# message . T... |
def run_outdated ( cls , options ) :
"""Print outdated user packages .""" | latest_versions = sorted ( cls . find_packages_latest_versions ( cls . options ) , key = lambda p : p [ 0 ] . project_name . lower ( ) )
for dist , latest_version , typ in latest_versions :
if latest_version > dist . parsed_version :
if options . all :
pass
elif options . pinned :
... |
def disable_node ( self , service_name , node_name ) :
"""Disables a given node name for the given service name via the
" disable server " HAProxy command .""" | logger . info ( "Disabling server %s/%s" , service_name , node_name )
return self . send_command ( "disable server %s/%s" % ( service_name , node_name ) ) |
def parse_transform ( transform_str ) :
"""Converts a valid SVG transformation string into a 3x3 matrix .
If the string is empty or null , this returns a 3x3 identity matrix""" | if not transform_str :
return np . identity ( 3 )
elif not isinstance ( transform_str , str ) :
raise TypeError ( 'Must provide a string to parse' )
total_transform = np . identity ( 3 )
transform_substrs = transform_str . split ( ')' ) [ : - 1 ]
# Skip the last element , because it should be empty
for substr i... |
def frontend_routing ( self , context ) :
"""Returns the targeted frontend and original state
: type context : satosa . context . Context
: rtype satosa . frontends . base . FrontendModule
: param context : The response context
: return : frontend""" | target_frontend = context . state [ STATE_KEY ]
satosa_logging ( logger , logging . DEBUG , "Routing to frontend: %s " % target_frontend , context . state )
context . target_frontend = target_frontend
frontend = self . frontends [ context . target_frontend ] [ "instance" ]
return frontend |
def item_links_addition ( self , data ) :
"""Add the links for each community .""" | links_item_factory = self . context . get ( 'links_item_factory' , default_links_item_factory )
data [ 'links' ] = links_item_factory ( data )
return data |
def tenant_quota_usages ( request , tenant_id = None , targets = None ) :
"""Get our quotas and construct our usage object .
: param tenant _ id : Target tenant ID . If no tenant _ id is provided ,
a the request . user . project _ id is assumed to be used .
: param targets : A tuple of quota names to be retri... | if not tenant_id :
tenant_id = request . user . project_id
disabled_quotas = get_disabled_quotas ( request , targets )
usages = QuotaUsage ( )
futurist_utils . call_functions_parallel ( ( _get_tenant_compute_usages , [ request , usages , disabled_quotas , tenant_id ] ) , ( _get_tenant_network_usages , [ request , u... |
def load_descendant_articles_for_section ( context , section , featured_in_homepage = None , featured_in_section = None , featured_in_latest = None , count = 5 ) :
"""Returns all descendant articles ( filtered using the parameters )
If the ` locale _ code ` in the context is not the main language , it will
retu... | request = context . get ( 'request' )
locale = context . get ( 'locale_code' )
page = section . get_main_language_page ( )
settings = SiteSettings . for_site ( request . site ) if request else None
qs = ArticlePage . objects . descendant_of ( page ) . filter ( language__is_main_language = True )
article_ordering = sett... |
def insertBefore ( self , child , beforeChild ) :
'''insertBefore - Inserts a child before # beforeChild
@ param child < AdvancedTag / str > - Child block to insert
@ param beforeChild < AdvancedTag / str > - Child block to insert before . if None , will be appended
@ return - The added child . Note , if it i... | # When the second arg is null / None , the node is appended . The argument is required per JS API , but null is acceptable . .
if beforeChild is None :
return self . appendBlock ( child )
# If # child is an AdvancedTag , we need to add it to both blocks and children .
isChildTag = isTagNode ( child )
myBlocks = sel... |
def _build_src_index ( self ) :
"""Build an indices for fast lookup of a source given its name
or coordinates .""" | self . _srcs = sorted ( self . _srcs , key = lambda t : t [ 'offset' ] )
nsrc = len ( self . _srcs )
radec = np . zeros ( ( 2 , nsrc ) )
for i , src in enumerate ( self . _srcs ) :
radec [ : , i ] = src . radec
self . _src_skydir = SkyCoord ( ra = radec [ 0 ] , dec = radec [ 1 ] , unit = u . deg )
self . _src_radiu... |
def __execute_sext ( self , instr ) :
"""Execute SEXT instruction .""" | op0_size = instr . operands [ 0 ] . size
op2_size = instr . operands [ 2 ] . size
op0_val = self . read_operand ( instr . operands [ 0 ] )
op0_msb = extract_sign_bit ( op0_val , op0_size )
op2_mask = ( 2 ** op2_size - 1 ) & ~ ( 2 ** op0_size - 1 ) if op0_msb == 1 else 0x0
op2_val = op0_val | op2_mask
self . write_opera... |
def _builtin_from_array_list ( required_type , value , list_level ) :
"""Helper method to make : func : ` from _ array _ list ` available to all classes extending this ,
without the need for additional imports .
: param required _ type : Type as what it should be parsed as . Any builtin .
: param value : The ... | return from_array_list ( required_type , value , list_level , is_builtin = True ) |
def next_chunk ( self ) :
"""Returns the chunk immediately following ( and adjacent to ) this one .""" | raise NotImplementedError ( "%s not implemented for %s" % ( self . next_chunk . __func__ . __name__ , self . __class__ . __name__ ) ) |
def flatten_blocks ( lines , num_indents = - 1 ) :
"""Take a list ( block ) or string ( statement ) and flattens it into a string
with indentation .""" | # The standard indent is four spaces
INDENTATION = " " * 4
if not lines :
return ""
# If this is a string , add the indentation and finish here
if isinstance ( lines , six . string_types ) :
return INDENTATION * num_indents + lines
# If this is not a string , join the lines and recurse
return "\n" . join ( [ fl... |
def MafMotifSelect ( mafblock , pwm , motif = None , threshold = 0 ) :
if motif != None and len ( motif ) != len ( pwm ) :
raise Exception ( "pwm and motif must be the same length" )
# generic alignment
alignlist = [ c . text for c in mafblock . components ]
align = pwmx . Align ( alignlist )
... | |
def get_region ( service , region , profile ) :
"""Retrieve the region for a particular AWS service based on configured region and / or profile .""" | _ , region , _ , _ = _get_profile ( service , region , None , None , profile )
return region |
def find_closest_calculated_frequencies ( input_freqs , metric_freqs ) :
"""Given a value ( or array ) of input frequencies find the closest values in
the list of frequencies calculated in the metric .
Parameters
input _ freqs : numpy . array or float
The frequency ( ies ) that you want to find the closest ... | try :
refEv = numpy . zeros ( len ( input_freqs ) , dtype = float )
except TypeError :
refEv = numpy . zeros ( 1 , dtype = float )
input_freqs = numpy . array ( [ input_freqs ] )
if len ( metric_freqs ) == 1 :
refEv [ : ] = metric_freqs [ 0 ]
return refEv
# FIXME : This seems complicated for what is... |
def sorted ( self ) :
"""Return a ( start , end ) tuple where start < = end .""" | if self . start < self . end :
return self . start , self . end
else :
return self . end , self . start |
def dumps ( self , cnf , ** kwargs ) :
"""Dump config ' cnf ' to a string .
: param cnf : Configuration data to dump
: param kwargs : optional keyword parameters to be sanitized : : dict
: return : string represents the configuration""" | kwargs = anyconfig . utils . filter_options ( self . _dump_opts , kwargs )
return self . dump_to_string ( cnf , ** kwargs ) |
def email_embed_image ( email , img_content_id , img_data ) :
"""email is a django . core . mail . EmailMessage object""" | img = MIMEImage ( img_data )
img . add_header ( 'Content-ID' , '<%s>' % img_content_id )
img . add_header ( 'Content-Disposition' , 'inline' )
email . attach ( img ) |
def deprecated ( func ) :
'''This is a decorator which can be used to mark functions
as deprecated . It will result in a warning being emitted
when the function is used .
https : / / wiki . python . org / moin / PythonDecoratorLibrary # Generating _ Deprecation _ Warnings''' | def new_func ( * args , ** kwargs ) :
warn ( "Call to deprecated function {}." . format ( func . __name__ ) , category = DeprecationWarning )
return func ( * args , ** kwargs )
new_func . __name__ = func . __name__
new_func . __doc__ = func . __doc__
new_func . __dict__ . update ( func . __dict__ )
return new_f... |
def plot_freq ( self , x , y , title = '' , ylabel = None , scale = 'semilogy' ) :
"""Plot mean frequency spectrum and display in dialog .
Parameters
x : list
vector with frequencies
y : ndarray
vector with amplitudes
title : str
plot title
ylabel : str
plot y label
scale : str
semilogy , logl... | freq = self . frequency
scaling = freq [ 'scaling' ] . get_value ( )
if ylabel is None :
if freq [ 'complex' ] . get_value ( ) :
ylabel = 'Amplitude (uV)'
elif 'power' == scaling :
ylabel = 'Power spectral density (uV ** 2 / Hz)'
elif 'energy' == scaling :
ylabel = 'Energy spectral d... |
def install_firmware ( self , firmware_information ) :
"""Installs firmware to a logical interconnect . The three operations that are supported for the firmware
update are Stage ( uploads firmware to the interconnect ) , Activate ( installs firmware on the interconnect ) ,
and Update ( which does a Stage and Ac... | firmware_uri = self . _helper . build_subresource_uri ( self . data [ "uri" ] , subresource_path = self . FIRMWARE_PATH )
return self . _helper . update ( firmware_information , firmware_uri ) |
def _read_with_sitk ( datapath ) :
"""Reads file using SimpleITK . Returns array of pixels ( image located in datapath ) and its metadata .
: param datapath : path to file ( img or dicom )
: return : tuple ( data3d , metadata ) , where data3d is array of pixels""" | try :
import SimpleITK as Sitk
except ImportError as e :
logger . error ( "Unable to import SimpleITK. On Windows try version 1.0.1" )
image = Sitk . ReadImage ( datapath )
data3d = dcmtools . get_pixel_array_from_sitk ( image )
# data3d , original _ dtype = dcmreaddata . get _ pixel _ array _ from _ dcmobj ( i... |
def set_clear_color ( self , color = 'black' , alpha = None ) :
"""Set the screen clear color
This is a wrapper for gl . glClearColor .
Parameters
color : str | tuple | instance of Color
Color to use . See vispy . color . Color for options .
alpha : float | None
Alpha to use .""" | self . glir . command ( 'FUNC' , 'glClearColor' , * Color ( color , alpha ) . rgba ) |
def _plot ( self ) :
"""Plot all dots for series""" | r_max = min ( self . view . x ( 1 ) - self . view . x ( 0 ) , ( self . view . y ( 0 ) or 0 ) - self . view . y ( 1 ) ) / ( 2 * 1.05 )
for serie in self . series :
self . dot ( serie , r_max ) |
def seqannotation ( self , seqrecord , allele , loc ) :
"""Gets the Annotation from the found sequence
: return : The Annotation from the found sequence
: rtype : Annotation""" | # seqrecord = self . seqrecord ( allele , loc )
complete_annotation = get_features ( seqrecord )
annotation = Annotation ( annotation = complete_annotation , method = 'match' , complete_annotation = True )
if self . alignments :
alignment = { f : self . annoated_alignments [ loc ] [ allele ] [ f ] [ 'Seq' ] for f i... |
def fix_fasta ( fasta ) :
"""remove pesky characters from fasta file header""" | for seq in parse_fasta ( fasta ) :
seq [ 0 ] = remove_char ( seq [ 0 ] )
if len ( seq [ 1 ] ) > 0 :
yield seq |
def symbol_list ( what_list ) :
'''provide default symbol lists
Parameters
what _ list : string
String name of symbol lists provided ; " list1 " , " list2 " ,
" lines1 " or " lines2 " .''' | if what_list is "list1" :
symbol = [ 'ro' , 'bo' , 'ko' , 'go' , 'mo' , 'r-' , 'b-' , 'k-' , 'g-' , 'm-' , 'r--' , 'b--' , 'k--' , 'g--' , 'r1' ]
# symbol = [ ' r + ' , ' ro ' , ' r - ' ]
elif what_list is "list2" :
symbol = [ 'r-' , 'b--' , 'g-.' , 'k:' , 'md' , '.' , 'o' , 'v' , '^' , '<' , '>' , '1' , '2... |
def standard_aggregation ( C ) :
"""Compute the sparsity pattern of the tentative prolongator .
Parameters
C : csr _ matrix
strength of connection matrix
Returns
AggOp : csr _ matrix
aggregation operator which determines the sparsity pattern
of the tentative prolongator
Cpts : array
array of Cpts ... | if not isspmatrix_csr ( C ) :
raise TypeError ( 'expected csr_matrix' )
if C . shape [ 0 ] != C . shape [ 1 ] :
raise ValueError ( 'expected square matrix' )
index_type = C . indptr . dtype
num_rows = C . shape [ 0 ]
Tj = np . empty ( num_rows , dtype = index_type )
# stores the aggregate # s
Cpts = np . empty ... |
def paint ( self , p , * args ) :
'''I have no idea why , but we need to generate the picture after painting otherwise
it draws incorrectly .''' | if self . picturenotgened :
self . generatePicture ( self . getBoundingParents ( ) [ 0 ] . rect ( ) )
self . picturenotgened = False
pg . ImageItem . paint ( self , p , * args )
self . generatePicture ( self . getBoundingParents ( ) [ 0 ] . rect ( ) ) |
def validate ( self , config ) :
"""Validate the given config against the ` Scheme ` .
Args :
config ( dict ) : The configuration to validate .
Raises :
errors . SchemeValidationError : The configuration fails
validation against the ` Schema ` .""" | if not isinstance ( config , dict ) :
raise errors . SchemeValidationError ( 'Scheme can only validate a dictionary config, but was given ' '{} (type: {})' . format ( config , type ( config ) ) )
for arg in self . args : # the option exists in the config
if arg . name in config :
arg . validate ( config... |
def cbpdn_class_label_lookup ( label ) :
"""Get a CBPDN class from a label string .""" | clsmod = { 'admm' : admm_cbpdn . ConvBPDN , 'fista' : fista_cbpdn . ConvBPDN }
if label in clsmod :
return clsmod [ label ]
else :
raise ValueError ( 'Unknown ConvBPDN solver method %s' % label ) |
def transaction ( commit = True ) :
"""Wrap a context with a commit / rollback .""" | try :
yield SessionContext . session
if commit :
SessionContext . session . commit ( )
except Exception :
if SessionContext . session :
SessionContext . session . rollback ( )
raise |
def subscribe ( self , event , hook ) :
"""Subscribe a callback to an event
Parameters
event : str
Available events are ' precall ' , ' postcall ' , and ' capacity ' .
precall is called with : ( connection , command , query _ kwargs )
postcall is called with : ( connection , command , query _ kwargs , res... | if hook not in self . _hooks [ event ] :
self . _hooks [ event ] . append ( hook ) |
def recount_view ( request ) :
"""Recount number _ of _ messages for all threads and number _ of _ responses for all requests .
Also set the change _ date for every thread to the post _ date of the latest message
associated with that thread .""" | requests_changed = 0
for req in Request . objects . all ( ) :
recount = Response . objects . filter ( request = req ) . count ( )
if req . number_of_responses != recount :
req . number_of_responses = recount
req . save ( )
requests_changed += 1
threads_changed = 0
for thread in Thread . ... |
def encode ( cls , s ) :
"""converts a plain text string to base64 encoding
: param s : unicode str | bytes , the base64 encoded string
: returns : unicode str""" | b = ByteString ( s )
be = base64 . b64encode ( b ) . strip ( )
return String ( be ) |
def _use_tables ( objs ) :
'''Whether a collection of Bokeh objects contains a TableWidget
Args :
objs ( seq [ Model or Document ] ) :
Returns :
bool''' | from . . models . widgets import TableWidget
return _any ( objs , lambda obj : isinstance ( obj , TableWidget ) ) |
def get ( cls , parent = None , id = None , data = None ) :
"""Inherit info from parent and return new object""" | # TODO - allow fetching of parent based on child ?
if parent is not None :
route = copy ( parent . route )
else :
route = { }
if id is not None and cls . ID_NAME is not None :
route [ cls . ID_NAME ] = id
obj = cls ( key = parent . key , route = route , config = parent . config )
if data : # This is used in... |
def add ( self , tid , result , role , session , oid = None , content = None , anony = None ) :
'''taobao . traderate . add 新增单个评价
新增单个评价 ( 注 : 在评价之前需要对订单成功的时间进行判定 ( end _ time ) , 如果超过15天 , 不能再通过该接口进行评价 )''' | request = TOPRequest ( 'taobao.traderate.add' )
request [ 'tid' ] = tid
request [ 'result' ] = result
request [ 'role' ] = role
if oid != None :
request [ 'oid' ] = oid
if content != None :
request [ 'content' ] = content
if anony != None :
request [ 'anony' ] = anony
self . create ( self . execute ( reques... |
def get ( self , blocking = True ) :
"""Gets a connection .
Args :
blocking : Whether to block when max _ size connections are already in use .
If false , may return None .
Returns :
A connection to the database .
Raises :
PoolAlreadyClosedError : if close ( ) method was already called on
this pool ... | if self . closed :
raise PoolAlreadyClosedError ( "Connection pool is already closed." )
# NOTE : Once we acquire capacity from the semaphore , it is essential that we
# return it eventually . On success , this responsibility is delegated to
# _ ConnectionProxy .
if not self . limiter . acquire ( blocking = blockin... |
def get_partial_DOS ( self ) :
"""Return frequency points and partial DOS as a tuple .
Projection is done to atoms and may be also done along directions
depending on the parameters at run _ partial _ dos .
Returns
A tuple with ( frequency _ points , partial _ dos ) .
frequency _ points : ndarray
shape =... | warnings . warn ( "Phonopy.get_partial_DOS is deprecated. " "Use Phonopy.get_projected_dos_dict." , DeprecationWarning )
pdos = self . get_projected_dos_dict ( )
return pdos [ 'frequency_points' ] , pdos [ 'projected_dos' ] |
def handle_dump ( args ) :
"""usage : cosmic - ray dump < session - file >
JSON dump of session data . This output is typically run through other
programs to produce reports .
Each line of output is a list with two elements : a WorkItem and a
WorkResult , both JSON - serialized . The WorkResult can be null ... | session_file = get_db_name ( args [ '<session-file>' ] )
with use_db ( session_file , WorkDB . Mode . open ) as database :
for work_item , result in database . completed_work_items :
print ( json . dumps ( ( work_item , result ) , cls = WorkItemJsonEncoder ) )
for work_item in database . pending_work_it... |
def cached_idxs ( method ) :
"""this function is used as a decorator for caching""" | def method_wrapper ( self , * args , ** kwargs ) :
tail = '_' . join ( str ( idx ) for idx in args )
_cache_attr_name = '_cache_' + method . __name__ + '_' + tail
_bool_attr_name = '_cached_' + method . __name__ + '_' + tail
is_cached = getattr ( self , _bool_attr_name )
if not is_cached :
r... |
def find_statements ( self , query , language = 'spo' , type = 'triples' , flush = None , limit = None ) :
"""Run a query in a format supported by the Fedora Resource Index ( e . g . , SPO
or Sparql ) and return the results .
: param query : query as a string
: param language : query language to use ; default... | http_args = { 'type' : type , 'lang' : language , 'query' : query , }
if type == 'triples' :
result_format = 'N-Triples'
elif type == 'tuples' :
result_format = 'CSV'
if limit is not None :
http_args [ 'limit' ] = limit
# else - error / exception ?
http_args [ 'format' ] = result_format
return self . _query... |
def swipe ( self , element , x , y , duration = None ) :
"""Swipe over an element
: param element : either a WebElement , PageElement or element locator as a tuple ( locator _ type , locator _ value )
: param x : horizontal movement
: param y : vertical movement
: param duration : time to take the swipe , i... | if not self . driver_wrapper . is_mobile_test ( ) :
raise Exception ( 'Swipe method is not implemented in Selenium' )
# Get center coordinates of element
center = self . get_center ( element )
initial_context = self . driver_wrapper . driver . current_context
if self . driver_wrapper . is_web_test ( ) or initial_co... |
def detect_r_peaks ( ecg_signal , sample_rate , time_units = False , volts = False , resolution = None , device = "biosignalsplux" , plot_result = False ) :
"""Brief
Python implementation of R peak detection algorithm ( proposed by Raja Selvaraj ) .
Description
Pan - Tompkins algorithm is one of the gold - st... | if volts is True :
if resolution is not None : # ecg _ signal = ( ( ecg _ signal / 2 * * resolution ) - 0.5 ) * 3
ecg_signal = raw_to_phy ( "ECG" , device , ecg_signal , resolution , option = "mV" )
else :
raise RuntimeError ( "For converting raw units to mV is mandatory the specification of " "... |
def users_for_perm ( cls , instance , perm_name , user_ids = None , group_ids = None , limit_group_permissions = False , skip_group_perms = False , db_session = None , ) :
"""return PermissionTuples for users AND groups that have given
permission for the resource , perm _ name is _ _ any _ permission _ _ then
u... | # noqa
db_session = get_db_session ( db_session , instance )
users_perms = resource_permissions_for_users ( cls . models_proxy , [ perm_name ] , [ instance . resource_id ] , user_ids = user_ids , group_ids = group_ids , limit_group_permissions = limit_group_permissions , skip_group_perms = skip_group_perms , db_session... |
def search_first ( self , * criterion , ** kwargs ) :
"""Returns the first match based on criteria or None .""" | query = self . _query ( * criterion )
query = self . _order_by ( query , ** kwargs )
query = self . _filter ( query , ** kwargs )
# NB : pagination must go last
query = self . _paginate ( query , ** kwargs )
return query . first ( ) |
def stupid_hack ( most = 10 , wait = None ) :
"""Return a random time between 1 - 10 Seconds .""" | # Stupid Hack For Public Cloud so it is not overwhelmed with API requests .
if wait is not None :
time . sleep ( wait )
else :
time . sleep ( random . randrange ( 1 , most ) ) |
def gpg_command ( args , env = None ) :
"""Prepare common GPG command line arguments .""" | if env is None :
env = os . environ
cmd = get_gnupg_binary ( neopg_binary = env . get ( 'NEOPG_BINARY' ) )
return [ cmd ] + args |
def send_apdu ( self , cla , ins , p1 , p2 , data = None , mrl = 0 , check_status = True ) :
"""Send an ISO / IEC 7816-4 APDU to the Type 4 Tag .
The 4 byte APDU header ( class , instruction , parameter 1 and 2)
is constructed from the first four parameters ( cla , ins , p1,
p2 ) without interpretation . The ... | apdu = bytearray ( [ cla , ins , p1 , p2 ] )
if not self . _extended_length_support :
if data and len ( data ) > 255 :
raise ValueError ( "unsupported command data length" )
if mrl and mrl > 256 :
raise ValueError ( "unsupported max response length" )
if data :
apdu += pack ( '>B' , ... |
def match_in_kwargs ( self , match_args , kwargs ) :
"""Matches against kwargs .""" | for match , default in match_args :
names = get_match_names ( match )
if names :
tempvar = self . get_temp_var ( )
self . add_def ( tempvar + " = " + "" . join ( kwargs + '.pop("' + name + '") if "' + name + '" in ' + kwargs + " else " for name in names ) + default , )
with self . down_a... |
def get_devices ( self , refresh = False , generic_type = None ) :
"""Get all devices from Abode .""" | if refresh or self . _devices is None :
if self . _devices is None :
self . _devices = { }
_LOGGER . info ( "Updating all devices..." )
response = self . send_request ( "get" , CONST . DEVICES_URL )
response_object = json . loads ( response . text )
if ( response_object and not isinstance ( ... |
def insert_tasks_ignore_duplicate_names ( tasks , queue , * args , ** kwargs ) :
"""Insert a batch of tasks into a specific queue . If a
DuplicateTaskNameError is raised , loop through the tasks and insert the
remaining , ignoring and logging the duplicate tasks .
Returns the number of successfully inserted t... | from google . appengine . api import taskqueue
try :
inserted = _insert_tasks ( tasks , queue , * args , ** kwargs )
return inserted
except taskqueue . DuplicateTaskNameError : # At least one task failed in our batch , attempt to re - insert the
# remaining tasks . Named tasks can never be transactional .
r... |
def get ( self , username , width = None , height = None ) :
"""Retrieve public details on a given user .
Note : Supplying the optional w or h parameters will result
in the ' custom ' photo URL being added to the ' profile _ image ' object :
: param username [ string ] : The user ’ s username . Required .
:... | url = "/users/{username}" . format ( username = username )
params = { "w" : width , "h" : height }
result = self . _get ( url , params = params )
return UserModel . parse ( result ) |
def findmin ( psr , method = 'Nelder-Mead' , history = False , formbats = False , renormalize = True , bounds = { } , ** kwargs ) :
"""Use scipy . optimize . minimize to find minimum - chisq timing solution ,
passing through all extra options . Resets psr [ . . . ] . val to the final solution ,
and returns the ... | ctr , err = psr . vals ( ) , psr . errs ( )
# to avoid losing precision , we ' re searching in units of parameter errors
if numpy . any ( err == 0.0 ) :
print ( "Warning: one or more fit parameters have zero a priori error, and won't be searched." )
hloc , hval = [ ] , [ ]
def func ( xs ) :
psr . vals ( [ c + x... |
def running_covar ( xx = True , xy = False , yy = False , remove_mean = False , symmetrize = False , sparse_mode = 'auto' , modify_data = False , column_selection = None , diag_only = False , nsave = 5 ) :
"""Returns a running covariance estimator
Returns an estimator object that can be fed chunks of X and Y data... | return RunningCovar ( compute_XX = xx , compute_XY = xy , compute_YY = yy , sparse_mode = sparse_mode , modify_data = modify_data , remove_mean = remove_mean , symmetrize = symmetrize , column_selection = column_selection , diag_only = diag_only , nsave = nsave ) |
def list_all_free_shipping_coupons ( cls , ** kwargs ) :
"""List FreeShippingCoupons
Return a list of FreeShippingCoupons
This method makes a synchronous HTTP request by default . To make an
asynchronous HTTP request , please pass async = True
> > > thread = api . list _ all _ free _ shipping _ coupons ( as... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'async' ) :
return cls . _list_all_free_shipping_coupons_with_http_info ( ** kwargs )
else :
( data ) = cls . _list_all_free_shipping_coupons_with_http_info ( ** kwargs )
return data |
def git_pretty ( ) :
"""returns a pretty summary of the commit or unkown if not in git repo""" | if git_repo ( ) is None :
return "unknown"
pretty = subprocess . check_output ( [ "git" , "log" , "--pretty=format:%h %s" , "-n" , "1" ] )
pretty = pretty . decode ( "utf-8" )
pretty = pretty . strip ( )
return pretty |
def porosimetry ( im , sizes = 25 , inlets = None , access_limited = True , mode = 'hybrid' ) :
r"""Performs a porosimetry simulution on the image
Parameters
im : ND - array
An ND image of the porous material containing True values in the
pore space .
sizes : array _ like or scalar
The sizes to invade .... | if im . ndim != im . squeeze ( ) . ndim :
warnings . warn ( 'Input image conains a singleton axis:' + str ( im . shape ) + ' Reduce dimensionality with np.squeeze(im) to avoid' + ' unexpected behavior.' )
dt = spim . distance_transform_edt ( im > 0 )
if inlets is None :
inlets = get_border ( im . shape , mode =... |
def satisfies ( self , other ) :
"""Check if the capabilities of a primitive are enough to satisfy a requirement .
Should be called on a Requirement that is acting as a
capability of a primitive . This method returning true means
that the capability advertised here is enough to handle
representing the data ... | if other . isnocare :
return True
if self . isnocare :
return False
if self . arbitrary :
return True
if self . constant and not other . arbitrary :
return True
if self . value is other . value and not other . arbitrary and not other . constant :
return True
return False |
def rounded_rectangle_region ( width , height , radius ) :
"""Returns a rounded rectangle wx . Region""" | bmp = wx . Bitmap . FromRGBA ( width , height )
# Mask color is # 00000
dc = wx . MemoryDC ( bmp )
dc . Brush = wx . Brush ( ( 255 , ) * 3 )
# Any non - black would do
dc . DrawRoundedRectangle ( 0 , 0 , width , height , radius )
dc . SelectObject ( wx . NullBitmap )
bmp . SetMaskColour ( ( 0 , ) * 3 )
return wx . Regi... |
def write_sequences_to_xlsx ( path , seqs ) :
"""Create a XLSX file listing the given sequences .
Arguments
path : str or pathlib . Path
The name of the file to create .
seqs : dict
A mapping of names to sequences , which can be either protein or DNA .""" | from openpyxl import Workbook
wb = Workbook ( )
ws = wb . active
for row , id in enumerate ( seqs , 1 ) :
ws . cell ( row , 1 ) . value = id
ws . cell ( row , 2 ) . value = seqs [ id ]
wb . save ( path ) |
def create_handlers_map ( prefix = '.*' ) :
"""Create new handlers map .
Args :
prefix : url prefix to use .
Returns :
list of ( regexp , handler ) pairs for WSGIApplication constructor .""" | return [ ( prefix + '/output' , _BarrierHandler ) , ( prefix + '/run' , _PipelineHandler ) , ( prefix + '/finalized' , _PipelineHandler ) , ( prefix + '/cleanup' , _CleanupHandler ) , ( prefix + '/abort' , _PipelineHandler ) , ( prefix + '/fanout' , _FanoutHandler ) , ( prefix + '/fanout_abort' , _FanoutAbortHandler ) ... |
def number_of_attributes ( self ) :
"""int : number of attributes .""" | if not self . _is_parsed :
self . _Parse ( )
self . _is_parsed = True
return len ( self . _attributes ) |
def confidenceInterval ( n , k , alpha = 0.68 , errorbar = False ) :
"""Given n tests and k successes , return efficiency and confidence interval .""" | try :
e = float ( k ) / float ( n )
except ZeroDivisionError :
return np . nan , [ np . nan , np . nan ]
bins = 1000001
dx = 1. / bins
efficiency = np . linspace ( 0 , 1 , bins )
# MODIFIED FOR LARGE NUMBERS
if n + 2 > 1000 :
a = gammalnStirling ( n + 2 )
else :
a = scipy . special . gammaln ( n + 2 )
i... |
def keyring_refresh ( ** kwargs ) :
"""Refresh the keyring in the cocaine - runtime .""" | ctx = Context ( ** kwargs )
ctx . execute_action ( 'keyring:refresh' , ** { 'tvm' : ctx . repo . create_secure_service ( 'tvm' ) , } ) |
def warn_or_error ( removal_version , deprecated_entity_description , hint = None , deprecation_start_version = None , stacklevel = 3 , frame_info = None , context = 1 , ensure_stderr = False ) :
"""Check the removal _ version against the current pants version .
Issues a warning if the removal version is > curren... | removal_semver = validate_deprecation_semver ( removal_version , 'removal version' )
if deprecation_start_version :
deprecation_start_semver = validate_deprecation_semver ( deprecation_start_version , 'deprecation start version' )
if deprecation_start_semver >= removal_semver :
raise InvalidSemanticVers... |
def compile ( definition , handlers = { } ) :
"""Generates validation function for validating JSON schema passed in ` ` definition ` ` .
Example :
. . code - block : : python
import fastjsonschema
validate = fastjsonschema . compile ( { ' type ' : ' string ' } )
validate ( ' hello ' )
This implementatio... | resolver , code_generator = _factory ( definition , handlers )
global_state = code_generator . global_state
# Do not pass local state so it can recursively call itself .
exec ( code_generator . func_code , global_state )
return global_state [ resolver . get_scope_name ( ) ] |
def anyword_substring_search ( target_words , query_words ) :
"""return True if all query _ words match""" | matches_required = len ( query_words )
matches_found = 0
for query_word in query_words :
reply = anyword_substring_search_inner ( query_word , target_words )
if reply is not False :
matches_found += 1
else : # this is imp , otherwise will keep checking
# when the final answer is already False
... |
def templateDoc ( self ) :
"""JSON serializable template to will all necessary details to recreate this
stimulus in another session .
: returns : dict""" | doc = dict ( self . componentDoc ( False ) . items ( ) + self . testDoc ( ) . items ( ) )
# go through auto - parameter selected components and use location index
autoparams = copy . deepcopy ( self . _autoParams . allData ( ) )
for p in autoparams :
selection = p [ 'selection' ]
serializable_selection = [ ]
... |
def reboot ( self , ** params ) :
"""Reboot outlet
Args :
params ( dict ) , must contain parameter " outlet " - outlet number
Example :
params = { ' outlet ' : 1}""" | outlet = params [ 'outlet' ]
# main menu
self . tn . write ( '\x1b\r\n' )
self . until_done ( )
# Device Manager
self . tn . write ( '1\r\n' )
self . until_done ( )
# Outlet Management
self . tn . write ( '2\r\n' )
self . until_done ( )
# Outlet Control
self . tn . write ( '1\r\n' )
self . until_done ( )
# Select outle... |
async def wait_for_body_middleware ( environ , start_response = None ) :
'''Use this middleware to wait for the full body .
This middleware wait for the full body to be received before letting
other middleware to be processed .
Useful when using synchronous web - frameworks such as : django : ` django < > ` .... | if environ . get ( 'wsgi.async' ) :
try :
chunk = await environ [ 'wsgi.input' ] . read ( )
except TypeError :
chunk = b''
environ [ 'wsgi.input' ] = BytesIO ( chunk )
environ . pop ( 'wsgi.async' ) |
def convertReadAlignment ( self , read , readGroupSet , readGroupId ) :
"""Convert a pysam ReadAlignment to a GA4GH ReadAlignment""" | samFile = self . getFileHandle ( self . _dataUrl )
# TODO fill out remaining fields
# TODO refine in tandem with code in converters module
ret = protocol . ReadAlignment ( )
# ret . fragmentId = ' TODO '
ret . aligned_quality . extend ( read . query_qualities )
ret . aligned_sequence = read . query_sequence
if SamFlags... |
def get_reply ( self , method , replyroot ) :
"""Process the I { reply } for the specified I { method } by unmarshalling it
into into Python object ( s ) .
@ param method : The name of the invoked method .
@ type method : str
@ param replyroot : The reply XML root node received after invoking the
specifie... | soapenv = replyroot . getChild ( "Envelope" , envns )
soapenv . promotePrefixes ( )
soapbody = soapenv . getChild ( "Body" , envns )
soapbody = self . multiref . process ( soapbody )
nodes = self . replycontent ( method , soapbody )
rtypes = self . returned_types ( method )
if len ( rtypes ) > 1 :
return self . rep... |
def _assemble_influence ( stmt ) :
"""Assemble an Influence statement into text .""" | subj_str = _assemble_agent_str ( stmt . subj . concept )
obj_str = _assemble_agent_str ( stmt . obj . concept )
# Note that n is prepended to increase to make it " an increase "
if stmt . subj . delta [ 'polarity' ] is not None :
subj_delta_str = ' decrease' if stmt . subj . delta [ 'polarity' ] == - 1 else 'n incr... |
def read_object_array ( f , data , options ) :
"""Reads an array of objects recursively .
Read the elements of the given HDF5 Reference array recursively
in the and constructs a ` ` numpy . object _ ` ` array from its elements ,
which is returned .
Parameters
f : h5py . File
The HDF5 file handle that is... | # Go through all the elements of data and read them using their
# references , and the putting the output in new object array .
data_derefed = np . zeros ( shape = data . shape , dtype = 'object' )
for index , x in np . ndenumerate ( data ) :
data_derefed [ index ] = read_data ( f , None , None , options , dsetgrp ... |
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