signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def uv_to_Rz ( u , v , delta = 1. , oblate = False ) :
"""NAME :
uv _ to _ Rz
PURPOSE :
calculate R and z from prolate confocal u and v coordinates
INPUT :
u - confocal u
v - confocal v
delta = focus
oblate = ( False ) if True , compute oblate confocal coordinates instead of prolate
OUTPUT :
( R... | if oblate :
R = delta * sc . cosh ( u ) * sc . sin ( v )
z = delta * sc . sinh ( u ) * sc . cos ( v )
else :
R = delta * sc . sinh ( u ) * sc . sin ( v )
z = delta * sc . cosh ( u ) * sc . cos ( v )
return ( R , z ) |
def get_route_to ( self , destination = "" , protocol = "" ) :
"""Return route details to a specific destination , learned from a certain protocol .""" | routes = { }
if not isinstance ( destination , py23_compat . string_types ) :
raise TypeError ( "Please specify a valid destination!" )
if protocol and isinstance ( destination , py23_compat . string_types ) :
protocol = protocol . lower ( )
if protocol == "connected" :
protocol = "direct"
# this is how is ... |
def coerce ( self , value , resource ) :
"""Coerce the value to an acceptable one .
Only these kinds of values are returned as is :
- str
- int
- float
- True
- False
- None
For all others values , it will be coerced using ` ` self . coerce _ default ` ` ( with convert the
value to a string in the... | if value in ( True , False , None ) :
return value
if isinstance ( value , ( int , float ) ) :
return value
if isinstance ( value , str ) :
return value
return self . coerce_default ( value , resource ) |
def remove ( self , name_or_klass ) :
"""Remove a extension from the editor .
: param name _ or _ klass : The name ( or class ) of the extension to remove .
: returns : The removed extension .""" | logger . debug ( 'removing extension {}' . format ( name_or_klass ) )
extension = self . get ( name_or_klass )
extension . on_uninstall ( )
self . _extensions . pop ( extension . name )
return extension |
def upsert ( queryset , model_objs , unique_fields , update_fields = None , returning = False , sync = False , ignore_duplicate_updates = True , return_untouched = False ) :
"""Perform a bulk upsert on a table , optionally syncing the results .
Args :
queryset ( Model | QuerySet ) : A model or a queryset that d... | queryset = queryset if isinstance ( queryset , models . QuerySet ) else queryset . objects . all ( )
model = queryset . model
# Populate automatically generated fields in the rows like date times
_fill_auto_fields ( model , model_objs )
# Sort the rows to reduce the chances of deadlock during concurrent upserts
model_o... |
def query ( cls , project = None , status = None , batch = None , parent = None , created_from = None , created_to = None , started_from = None , started_to = None , ended_from = None , ended_to = None , offset = None , limit = None , order_by = None , order = None , api = None ) :
"""Query ( List ) tasks . Date pa... | api = api or cls . _API
if parent :
parent = Transform . to_task ( parent )
if project :
project = Transform . to_project ( project )
if created_from :
created_from = Transform . to_datestring ( created_from )
if created_to :
created_to = Transform . to_datestring ( created_to )
if started_from :
st... |
def strip_msa_100 ( msa , threshold , plot = False ) :
"""strip out columns of a MSA that represent gaps for X percent ( threshold ) of sequences""" | msa = [ seq for seq in parse_fasta ( msa ) ]
columns = [ [ 0 , 0 ] for pos in msa [ 0 ] [ 1 ] ]
# [ [ # bases , # gaps ] , [ # bases , # gaps ] , . . . ]
for seq in msa :
for position , base in enumerate ( seq [ 1 ] ) :
if base == '-' or base == '.' :
columns [ position ] [ 1 ] += 1
else... |
def get_path ( self , wd ) :
"""Returns the path associated to WD , if WD is unknown it returns None .
@ param wd : Watch descriptor .
@ type wd : int
@ return : Path or None .
@ rtype : string or None""" | watch_ = self . _wmd . get ( wd )
if watch_ is not None :
return watch_ . path |
def update_search_window ( self , search_window , x_center , y_center ) :
"""update the search area for the lens equation solver
: param search _ window : search _ window : window size of the image position search with the lens equation solver .
: param x _ center : center of search window
: param y _ center ... | self . _search_window , self . _x_center , self . _y_center = search_window , x_center , y_center |
def construct_eventstore ( config , section = None ) :
"""Construct the event store to write and write from / to .
The event store is constructed from an optionally given configuration file
and / or command line arguments . Command line arguments has higher
presendence over configuration file attributes .
I... | ESTORE_CLASS_ATTRIBUTE = 'class'
if config is None :
_logger . warn ( "Using InMemoryEventStore. Events are not persisted." " See example config file on how to persist them." )
# XXX : This is to evade circular dependency between config and
# eventstores .
import rewind . server . eventstores as eventst... |
def get_pending_transfer_pairs ( transfers_pair : List [ MediationPairState ] , ) -> List [ MediationPairState ] :
"""Return the transfer pairs that are not at a final state .""" | pending_pairs = list ( pair for pair in transfers_pair if pair . payee_state not in STATE_TRANSFER_FINAL or pair . payer_state not in STATE_TRANSFER_FINAL )
return pending_pairs |
def copy ( self , ** kwargs ) :
""": param kwargs :
: return : copy of this object modifying the kwargs""" | for k in kwargs :
assert k in self . _keys , 'Invalid key: %s' % k
d = self . values ( )
d . update ( kwargs )
return self . __class__ ( ** d ) |
def _flush ( self ) :
"""Flush all caches
Might be used after classes , methods or fields are added .""" | self . classes_names = None
self . __cache_methods = None
self . __cached_methods_idx = None
self . __cache_fields = None
# cache methods and fields as well , otherwise the decompiler is quite slow
self . __cache_all_methods = None
self . __cache_all_fields = None |
def add_firewall_rule ( self , direction , action , src = None , dst = None ) :
"""Adds a firewall rule to the router .
The TunTap router includes a very simple firewall for governing vassal ' s traffic .
The first matching rule stops the chain , if no rule applies , the policy is " allow " .
: param str | un... | value = [ action ]
if src :
value . extend ( ( src , dst ) )
self . _set_aliased ( 'router-firewall-%s' % direction . lower ( ) , ' ' . join ( value ) , multi = True )
return self |
def seat_button_count ( self ) :
"""The total number of buttons pressed on all devices on
the associated seat after the the event was triggered .
For events that are not of type
: attr : ` ~ libinput . constant . EventType . TABLET _ TOOL _ BUTTON ` , this property
raises : exc : ` AttributeError ` .
Retu... | if self . type != EventType . TABLET_TOOL_BUTTON :
raise AttributeError ( _wrong_prop . format ( self . type ) )
return self . _libinput . libinput_event_tablet_tool_get_seat_button_count ( self . _handle ) |
def walk ( self , cli ) :
"""Walk through children .""" | yield self
for c in self . children :
for i in c . walk ( cli ) :
yield i |
def export_comps ( request ) :
"""Returns a zipfile of the rendered HTML templates in the COMPS _ DIR""" | in_memory = BytesIO ( )
zip = ZipFile ( in_memory , "a" )
comps = settings . COMPS_DIR
static = settings . STATIC_ROOT or ""
context = RequestContext ( request , { } )
context [ 'debug' ] = False
# dump static resources
# TODO : inspect each template and only pull in resources that are used
for dirname , dirs , filenam... |
def add ( self , txt , indent = 0 ) :
"""Adds some text , no newline will be appended .
The text can be indented with the optional argument ' indent ' .""" | if isinstance ( txt , unicode ) :
try :
txt = str ( txt )
except UnicodeEncodeError :
s = [ ]
for c in txt :
try :
s . append ( str ( c ) )
except UnicodeEncodeError :
s . append ( repr ( c ) )
txt = '' . join ( s )
self . t... |
def getSensorData ( self , name , channel = None ) :
"""Returns a sensor node""" | return self . _getNodeData ( name , self . _SENSORNODE , channel ) |
def split_and_load ( arrs , ctx ) :
"""split and load arrays to a list of contexts""" | assert isinstance ( arrs , ( list , tuple ) )
# split and load
loaded_arrs = [ mx . gluon . utils . split_and_load ( arr , ctx , even_split = False ) for arr in arrs ]
return zip ( * loaded_arrs ) |
def rewrite_file_imports ( item , vendored_libs , vendor_dir ) :
"""Rewrite ' import xxx ' and ' from xxx import ' for vendored _ libs""" | text = item . read_text ( encoding = 'utf-8' )
renames = LIBRARY_RENAMES
for k in LIBRARY_RENAMES . keys ( ) :
if k not in vendored_libs :
vendored_libs . append ( k )
for lib in vendored_libs :
to_lib = lib
if lib in renames :
to_lib = renames [ lib ]
text = re . sub ( r'([\n\s]*)import... |
def get_main_activities ( self ) :
"""Return names of the main activities
These values are read from the AndroidManifest . xml
: rtype : a set of str""" | x = set ( )
y = set ( )
for i in self . xml :
if self . xml [ i ] is None :
continue
activities_and_aliases = self . xml [ i ] . findall ( ".//activity" ) + self . xml [ i ] . findall ( ".//activity-alias" )
for item in activities_and_aliases : # Some applications have more than one MAIN activity .
... |
def _handle_double_click ( self , event ) :
"""Double click with left mouse button focuses the state and toggles the collapse status""" | if event . get_button ( ) [ 1 ] == 1 : # Left mouse button
path_info = self . view . tree_view . get_path_at_pos ( int ( event . x ) , int ( event . y ) )
if path_info : # Valid entry was clicked on
path = path_info [ 0 ]
item_iter = self . tree_store . get_iter ( path )
# Toggle collaps... |
def instance ( self , instance_id , display_name = None , instance_type = None , labels = None ) :
"""Factory to create a instance associated with this client .
For example :
. . literalinclude : : snippets . py
: start - after : [ START bigtable _ create _ prod _ instance ]
: end - before : [ END bigtable ... | return Instance ( instance_id , self , display_name = display_name , instance_type = instance_type , labels = labels , ) |
def _scan_for_tokens ( contents ) :
"""Scan a string for tokens and return immediate form tokens .""" | # Regexes are in priority order . Changing the order may alter the
# behavior of the lexer
scanner = re . Scanner ( [ # Things inside quotes
( r"(?<![^\s\(])([\"\'])(?:(?=(\\?))\2.)*?\1(?![^\s\)])" , lambda s , t : ( TokenType . QuotedLiteral , t ) ) , # Numbers on their own
( r"(?<![^\s\(])-?[0-9]+(?![^\s\)\(])" , lam... |
def _message ( self ) :
"""get the message payload""" | filepath = self . _record . file_path
try :
return load_message ( filepath )
except FileNotFoundError :
expire_file ( filepath )
empty = email . message . Message ( )
empty . set_payload ( '' )
return empty |
def register_filter_builder ( self , function , ** kwargs ) :
"""Register a filter function with this : class : ` ~ . Filters ` instance .
This function is curried with : class : ` ~ okcupyd . util . currying . curry `
- - that is , it can be invoked partially before it is fully evaluated .
This allows us to ... | kwargs [ 'transform' ] = function
if kwargs . get ( 'decider' ) :
kwargs [ 'decide' ] = kwargs . get ( 'decider' )
return type ( 'filter' , ( self . filter_class , ) , kwargs ) |
def clone ( self , path = None , * , with_contents = True , ** options ) :
"""Clone the file .""" | file = File ( path if path else self . path , cwd = options . get ( "cwd" , self . cwd ) )
file . base = options . get ( "base" , self . base )
if with_contents :
file . contents = options . get ( "contents" , self . contents )
return file |
def parse_global_args ( argv ) :
"""Parse all global iotile tool arguments .
Any flag based argument at the start of the command line is considered as
a global flag and parsed . The first non flag argument starts the commands
that are passed to the underlying hierarchical shell .
Args :
argv ( list ) : Th... | parser = create_parser ( )
args = parser . parse_args ( argv )
should_log = args . include or args . exclude or ( args . verbose > 0 )
verbosity = args . verbose
root = logging . getLogger ( )
if should_log :
formatter = logging . Formatter ( '%(asctime)s.%(msecs)03d %(levelname).3s %(name)s %(message)s' , '%y-%m-%... |
def _make_grid_of_axes ( self , bounding_rect = cfg . bounding_rect_default , num_rows = cfg . num_rows_per_view_default , num_cols = cfg . num_cols_grid_default , axis_pad = cfg . axis_pad_default , commn_annot = None , ** axis_kwargs ) :
"""Creates a grid of axes bounded within a given rectangle .""" | axes_in_grid = list ( )
extents = self . _compute_cell_extents_grid ( bounding_rect = bounding_rect , num_cols = num_cols , num_rows = num_rows , axis_pad = axis_pad )
for cell_ext in extents :
ax_cell = self . fig . add_axes ( cell_ext , frameon = False , visible = False , ** axis_kwargs )
if commn_annot is no... |
def execute_action_list ( obj , target , kw ) :
"""Actually execute the action list .""" | env = obj . get_build_env ( )
kw = obj . get_kw ( kw )
status = 0
for act in obj . get_action_list ( ) :
args = ( [ ] , [ ] , env )
status = act ( * args , ** kw )
if isinstance ( status , SCons . Errors . BuildError ) :
status . executor = obj
raise status
elif status :
msg = "E... |
async def on_raw_375 ( self , message ) :
"""Start message of the day .""" | await self . _registration_completed ( message )
self . motd = message . params [ 1 ] + '\n' |
def list_domains ( ) :
'''Return a list of virtual machine names on the minion
CLI Example :
. . code - block : : bash
salt ' * ' virt . list _ domains''' | with _get_xapi_session ( ) as xapi :
hosts = xapi . VM . get_all ( )
ret = [ ]
for _host in hosts :
if xapi . VM . get_record ( _host ) [ 'is_control_domain' ] is False :
ret . append ( xapi . VM . get_name_label ( _host ) )
return ret |
def as4_capability ( self , ** kwargs ) :
"""Set Spanning Tree state .
Args :
enabled ( bool ) : Is AS4 Capability enabled ? ( True , False )
callback ( function ) : A function executed upon completion of the
method . The only parameter passed to ` callback ` will be the
` ` ElementTree ` ` ` config ` .
... | enabled = kwargs . pop ( 'enabled' , True )
callback = kwargs . pop ( 'callback' , self . _callback )
if not isinstance ( enabled , bool ) :
raise ValueError ( '%s must be `True` or `False`.' % repr ( enabled ) )
as4_capability_args = dict ( vrf_name = kwargs . pop ( 'vrf' , 'default' ) , rbridge_id = kwargs . pop ... |
def bitset ( name , members , base = bases . BitSet , list = False , tuple = False ) :
"""Return a new bitset class with given name and members .
Args :
name : Name of the class to be created .
members : Hashable sequence of allowed bitset members .
base : Base class to derive the returned class from .
li... | if not name :
raise ValueError ( 'empty bitset name: %r' % name )
if not hasattr ( members , '__getitem__' ) or not hasattr ( members , '__len__' ) :
raise ValueError ( 'non-sequence bitset members: %r' % members )
if not len ( members ) :
raise ValueError ( 'less than one bitset member: %r' % ( members , )... |
def _create_tokens_for_next_line_dent ( self , newline_token ) :
"""Starting from a newline token that isn ' t followed by another newline
token , returns any indent or dedent tokens that immediately follow .
If indentation doesn ' t change , returns None .""" | indent_delta = self . _get_next_line_indent_delta ( newline_token )
if indent_delta is None or indent_delta == 0 : # Next line ' s indent isn ' t relevant OR there was no change in
# indentation .
return None
dent_type = 'INDENT' if indent_delta > 0 else 'DEDENT'
dent_token = _create_token ( dent_type , '\t' , newl... |
def scrape_file ( self , file , encoding = None , base_url = None ) :
'''Scrape a file for links .
See : meth : ` scrape ` for the return value .''' | elements = self . iter_elements ( file , encoding = encoding )
link_contexts = set ( )
link_infos = self . _element_walker . iter_links ( elements )
for link_info in link_infos :
element_base_url = base_url
if link_info . base_link :
clean_base_url = clean_link_soup ( link_info . base_link )
if ... |
def virt_env ( self ) :
"""Getter for this instance ' s virt env , creates it if needed
Returns :
lago . virt . VirtEnv : virt env instance used by this prefix""" | if self . _virt_env is None :
self . _virt_env = self . _create_virt_env ( )
return self . _virt_env |
def get_monitors ( self ) -> List [ Monitor ] :
"""Get a list of Monitors from the ZoneMinder API .""" | raw_monitors = self . _zm_request ( 'get' , ZoneMinder . MONITOR_URL )
if not raw_monitors :
_LOGGER . warning ( "Could not fetch monitors from ZoneMinder" )
return [ ]
monitors = [ ]
for raw_result in raw_monitors [ 'monitors' ] :
_LOGGER . debug ( "Initializing camera %s" , raw_result [ 'Monitor' ] [ 'Id'... |
def export_mesh ( vertices , triangles , filename , mesh_name = "mcubes_mesh" ) :
"""Exports a mesh in the COLLADA ( . dae ) format .
Needs PyCollada ( https : / / github . com / pycollada / pycollada ) .""" | import collada
mesh = collada . Collada ( )
vert_src = collada . source . FloatSource ( "verts-array" , vertices , ( 'X' , 'Y' , 'Z' ) )
geom = collada . geometry . Geometry ( mesh , "geometry0" , mesh_name , [ vert_src ] )
input_list = collada . source . InputList ( )
input_list . addInput ( 0 , 'VERTEX' , "#verts-arr... |
def _inject ( self , value , settings ) :
"""Inject ` ` settings ` ` into ` ` value ` ` .
Go through ` ` value ` ` looking for ` ` { { NAME } } ` ` groups and replace
each group with the value of the named item from ` ` settings ` ` .
Args :
value ( str ) : The value to inject settings into
settings : An ... | assert isinstance ( value , string_types ) , 'Expected str; got {0.__class__}' . format ( value )
begin , end = '{{' , '}}'
if begin not in value :
return value , False
new_value = value
begin_pos , end_pos = 0 , None
len_begin , len_end = len ( begin ) , len ( end )
len_value = len ( new_value )
while begin_pos < ... |
def bipartition ( seq ) :
"""Return a list of bipartitions for a sequence .
Args :
a ( Iterable ) : The sequence to partition .
Returns :
list [ tuple [ tuple ] ] : A list of tuples containing each of the two
partitions .
Example :
> > > bipartition ( ( 1,2,3 ) )
[ ( ( ) , ( 1 , 2 , 3 ) ) , ( ( 1 , ... | return [ ( tuple ( seq [ i ] for i in part0_idx ) , tuple ( seq [ j ] for j in part1_idx ) ) for part0_idx , part1_idx in bipartition_indices ( len ( seq ) ) ] |
def request_restart ( self , req , msg ) :
"""Restart the device server .
Returns
success : { ' ok ' , ' fail ' }
Whether scheduling the restart succeeded .
Examples
? restart
! restart ok""" | if self . _restart_queue is None :
raise FailReply ( "No restart queue registered -- cannot restart." )
f = tornado_Future ( )
@ gen . coroutine
def _restart ( ) : # . put should never block because queue should have no size limit
self . _restart_queue . put_nowait ( self )
req . reply ( 'ok' )
raise As... |
def repair_duplicate_names ( self ) :
"""Prior to 1101.1.1 , pmxbot would incorrectly create new karma records
for individuals with multiple names .
This routine corrects those records .""" | for name in self . _all_names ( ) :
cur = self . db . find ( { 'names' : name } )
main_doc = next ( cur )
for duplicate in cur :
query = { '_id' : main_doc [ '_id' ] }
update = { '$inc' : { 'value' : duplicate [ 'value' ] } , '$push' : { 'names' : { '$each' : duplicate [ 'names' ] } } , }
... |
def loads_config ( s , parser_params = JSONParserParams ( ) , string_to_scalar_converter = DefaultStringToScalarConverter ( ) ) :
"""Works similar to the loads ( ) function but this one returns a json object hierarchy
that wraps all json objects , arrays and scalars to provide a nice config query syntax .
For e... | parser = JSONParser ( parser_params )
object_builder_params = ConfigObjectBuilderParams ( string_to_scalar_converter = string_to_scalar_converter )
listener = ObjectBuilderParserListener ( object_builder_params )
parser . parse ( s , listener )
return listener . result |
def context_chunks ( self , context ) :
"""Retrieves all tokens , divided into the chunks in context ` ` context ` ` .
Parameters
context : str
Context name .
Returns
chunks : list
Each item in ` ` chunks ` ` is a list of tokens .""" | N_chunks = len ( self . contexts [ context ] )
chunks = [ ]
for j in xrange ( N_chunks ) :
chunks . append ( self . context_chunk ( context , j ) )
return chunks |
def Presentation ( pptx = None ) :
"""Return a | Presentation | object loaded from * pptx * , where * pptx * can be
either a path to a ` ` . pptx ` ` file ( a string ) or a file - like object . If
* pptx * is missing or ` ` None ` ` , the built - in default presentation
" template " is loaded .""" | if pptx is None :
pptx = _default_pptx_path ( )
presentation_part = Package . open ( pptx ) . main_document_part
if not _is_pptx_package ( presentation_part ) :
tmpl = "file '%s' is not a PowerPoint file, content type is '%s'"
raise ValueError ( tmpl % ( pptx , presentation_part . content_type ) )
return pr... |
def parse ( station : str , txt : str ) -> ( MetarData , Units ) : # type : ignore
"""Returns MetarData and Units dataclasses with parsed data and their associated units""" | core . valid_station ( station )
return parse_na ( txt ) if core . uses_na_format ( station [ : 2 ] ) else parse_in ( txt ) |
def ICCdecode ( s ) :
"""Take an ICC encoded tag , and dispatch on its type signature
( first 4 bytes ) to decode it into a Python value . Pair ( * sig * ,
* value * ) is returned , where * sig * is a 4 byte string , and * value * is
some Python value determined by the content and type .""" | sig = s [ 0 : 4 ] . strip ( )
f = dict ( text = RDtext , XYZ = RDXYZ , curv = RDcurv , vcgt = RDvcgt , sf32 = RDsf32 , )
if sig not in f :
return None
return ( sig , f [ sig ] ( s ) ) |
def first_child_found_in ( self , * tagnames ) :
"""Return the first child found with tag in * tagnames * , or None if
not found .""" | for tagname in tagnames :
child = self . find ( qn ( tagname ) )
if child is not None :
return child
return None |
def time_to_hhmmssmmm ( time_value , decimal_separator = "." ) :
"""Format the given time value into a ` ` HH : MM : SS . mmm ` ` string .
Examples : : :
12 = > 00:00:12.000
12.345 = > 00:00:12.345
12.345432 = > 00:00:12.345
12.345678 = > 00:00:12.346
83 = > 00:01:23.000
83.456 = > 00:01:23.456
83.4... | if time_value is None :
time_value = 0
tmp = time_value
hours = int ( math . floor ( tmp / 3600 ) )
tmp -= ( hours * 3600 )
minutes = int ( math . floor ( tmp / 60 ) )
tmp -= minutes * 60
seconds = int ( math . floor ( tmp ) )
tmp -= seconds
milliseconds = int ( math . floor ( tmp * 1000 ) )
return "%02d:%02d:%02d%... |
def dependencies_of ( self , address ) :
"""Returns the dependencies of the Target at ` address ` .
This method asserts that the address given is actually in the BuildGraph .
: API : public""" | assert address in self . _target_by_address , ( 'Cannot retrieve dependencies of {address} because it is not in the BuildGraph.' . format ( address = address ) )
return self . _target_dependencies_by_address [ address ] |
def _listFilesPosix ( self ) -> [ 'File' ] :
"""List Files for POSIX
Search and list the files and folder in the current directory for the
POSIX file system .
@ return : List of directory files and folders .""" | find = "find %s -type f" % self . _path
output = check_output ( args = find . split ( ) ) . strip ( ) . decode ( ) . split ( '\n' )
return output |
def _select_ontology ( self , line ) :
"""try to select an ontology NP : the actual load from FS is in < _ load _ ontology >""" | try :
var = int ( line )
# it ' s a string
if var in range ( 1 , len ( self . all_ontologies ) + 1 ) :
self . _load_ontology ( self . all_ontologies [ var - 1 ] )
except ValueError :
out = [ ]
for each in self . all_ontologies :
if line in each :
out += [ each ]
choic... |
def value_to_string ( self , obj ) :
"""Ensure data is serialized correctly .""" | value = self . value_from_object ( obj )
return self . get_prep_value ( value ) |
def mk_nested_dic ( path , val , seps = PATH_SEPS ) :
"""Make a nested dict iteratively .
: param path : Path expression to make a nested dict
: param val : Value to set
: param seps : Separator char candidates
> > > mk _ nested _ dic ( " a . b . c " , 1)
{ ' a ' : { ' b ' : { ' c ' : 1 } } }
> > > mk _... | ret = None
for key in reversed ( _split_path ( path , seps ) ) :
ret = { key : val if ret is None else ret . copy ( ) }
return ret |
def number ( items ) :
"""Maps numbering onto given values""" | n = len ( items )
if n == 0 :
return items
places = str ( int ( math . log10 ( n ) // 1 + 1 ) )
format = '[{0[0]:' + str ( int ( places ) ) + 'd}] {0[1]}'
return map ( lambda x : format . format ( x ) , enumerate ( items ) ) |
def __get_sigmas ( self ) :
"""will populate the stack _ sigma dictionary with the energy and sigma array
for all the compound / element and isotopes""" | stack_sigma = { }
_stack = self . stack
_file_path = os . path . abspath ( os . path . dirname ( __file__ ) )
_database_folder = os . path . join ( _file_path , 'reference_data' , self . database )
_list_compounds = _stack . keys ( )
for _compound in _list_compounds :
_list_element = _stack [ _compound ] [ 'element... |
def get ( self ) :
"""API endpoint to retrieve a list of links to transaction
outputs .
Returns :
A : obj : ` list ` of : cls : ` str ` of links to outputs .""" | parser = reqparse . RequestParser ( )
parser . add_argument ( 'public_key' , type = parameters . valid_ed25519 , required = True )
parser . add_argument ( 'spent' , type = parameters . valid_bool )
args = parser . parse_args ( strict = True )
pool = current_app . config [ 'bigchain_pool' ]
with pool ( ) as bigchain :
... |
def cache_nodes ( gir_root , all_girs ) :
'''Identify and store all the gir symbols the symbols we will document
may link to , or be typed with''' | ns_node = gir_root . find ( './{%s}namespace' % NS_MAP [ 'core' ] )
id_prefixes = ns_node . attrib [ '{%s}identifier-prefixes' % NS_MAP [ 'c' ] ]
sym_prefixes = ns_node . attrib [ '{%s}symbol-prefixes' % NS_MAP [ 'c' ] ]
id_key = '{%s}identifier' % NS_MAP [ 'c' ]
for node in gir_root . xpath ( './/*[@c:identifier]' , n... |
def get_alert_log ( self , current = 0 , minimum = 0 , maximum = 100 , header = "" , action_key = None ) :
"""Get the alert log .""" | return self . get_alert ( current = current , minimum = minimum , maximum = maximum , header = header , action_key = action_key , log = True ) |
def _get_names ( dirs ) :
"""Get alphabet and label names , union across all dirs .""" | alphabets = set ( )
label_names = { }
for d in dirs :
for example in _walk_omniglot_dir ( d ) :
alphabet , alphabet_char_id , label , _ = example
alphabets . add ( alphabet )
label_name = "%s_%d" % ( alphabet , alphabet_char_id )
if label in label_names :
assert label_nam... |
def get_value ( self ) :
"""Return memory usage .""" | from spyder . utils . system import memory_usage
text = '%d%%' % memory_usage ( )
return 'Mem ' + text . rjust ( 3 ) |
def project_clone ( object_id , input_params = { } , always_retry = False , ** kwargs ) :
"""Invokes the / project - xxxx / clone API method .
For more info , see : https : / / wiki . dnanexus . com / API - Specification - v1.0.0 / Cloning # API - method % 3A - % 2Fclass - xxxx % 2Fclone""" | return DXHTTPRequest ( '/%s/clone' % object_id , input_params , always_retry = always_retry , ** kwargs ) |
def parse_modes ( modes , current , behaviour ) :
"""Parse mode change string ( s ) and return updated dictionary .""" | current = current . copy ( )
modes = modes [ : ]
# Iterate in a somewhat odd way over the list because we want to modify it during iteration .
i = 0
while i < len ( modes ) :
piece = modes [ i ]
add = True
sigiled = False
for mode in piece : # Set mode to addition or deletion of modes .
if mode ... |
def add_resource_types ( resource_i , types ) :
"""Save a reference to the types used for this resource .
@ returns a list of type _ ids representing the type ids
on the resource .""" | if types is None :
return [ ]
existing_type_ids = [ ]
if resource_i . types :
for t in resource_i . types :
existing_type_ids . append ( t . type_id )
new_type_ids = [ ]
for templatetype in types :
if templatetype . id in existing_type_ids :
continue
rt_i = ResourceType ( )
rt_i . ty... |
def wash_url_argument ( var , new_type ) :
"""Wash argument into ' new _ type ' , that can be ' list ' , ' str ' ,
' int ' , ' tuple ' or ' dict ' .
If needed , the check ' type ( var ) is not None ' should be done before
calling this function .
@ param var : variable value
@ param new _ type : variable t... | out = [ ]
if new_type == 'list' : # return lst
if isinstance ( var , list ) :
out = var
else :
out = [ var ]
elif new_type == 'str' : # return str
if isinstance ( var , list ) :
try :
out = "%s" % var [ 0 ]
except :
out = ""
elif isinstance ( var ,... |
def get_branches ( path ) :
"""获取当前所有分支名称的列表 。
: param str path : git 仓库文件夹路径 。
: return : 分支名称列表 。 当前分支位于列表第一项 。
: rtype : list""" | code , output = call ( path , 'branch' , '--list' )
if code > 0 :
return None
branches = output . split ( '\n' )
newbr = [ None ]
for br in branches :
if br :
if br [ 0 ] == '*' :
newbr [ 0 ] = br [ 2 : ]
else :
newbr . append ( br [ 2 : ] )
return newbr |
async def create_link ( project , nodes ) :
"""Create all possible link of a node""" | node1 = random . choice ( list ( nodes . values ( ) ) )
for port in range ( 0 , 8 ) :
node2 = random . choice ( list ( nodes . values ( ) ) )
if node1 == node2 :
continue
data = { "nodes" : [ { "adapter_number" : 0 , "node_id" : node1 [ "node_id" ] , "port_number" : port } , { "adapter_number" : 0 ,... |
def on_event_pre ( self , e : Event ) -> None :
"""Set values set on browser before calling event listeners .""" | super ( ) . on_event_pre ( e )
ct_msg = e . init . get ( 'currentTarget' , dict ( ) )
if e . type in ( 'input' , 'change' ) : # Update user inputs
self . _set_text_content ( ct_msg . get ( 'value' ) or '' ) |
def transport_closed ( self , ** kwargs ) :
"""Called by Transports when they close unexpectedly , not as a result of
Connection . disconnect ( ) .
TODO : document args""" | msg = 'unknown cause'
self . logger . warning ( 'transport to %s closed : %s' % ( self . _host , kwargs . get ( 'msg' , msg ) ) )
self . _close_info = { 'reply_code' : kwargs . get ( 'reply_code' , 0 ) , 'reply_text' : kwargs . get ( 'msg' , msg ) , 'class_id' : kwargs . get ( 'class_id' , 0 ) , 'method_id' : kwargs . ... |
def align_transcriptome ( fastq_file , pair_file , ref_file , data ) :
"""bwa mem with settings for aligning to the transcriptome for eXpress / RSEM / etc""" | work_bam = dd . get_work_bam ( data )
base , ext = os . path . splitext ( work_bam )
out_file = base + ".transcriptome" + ext
if utils . file_exists ( out_file ) :
data = dd . set_transcriptome_bam ( data , out_file )
return data
# bwa mem needs phred + 33 quality , so convert if it is Illumina
if dd . get_qual... |
def create ( curve , data ) :
"""Creates EC keypair from the just secret key and curve name
@ param curve - name of elliptic curve
@ param num - byte array or long number representing key""" | ec_key = libcrypto . EC_KEY_new_by_curve_name ( curve . nid )
if ec_key is None :
raise PKeyError ( "EC_KEY_new_by_curvename" )
group = libcrypto . EC_KEY_get0_group ( ec_key )
if group is None :
raise PKeyError ( "EC_KEY_get0_group" )
libcrypto . EC_GROUP_set_asn1_flag ( group , 1 )
raw_key = libcrypto . BN_ne... |
def get_SCAT_points ( x_Arai_segment , y_Arai_segment , tmin , tmax , ptrm_checks_temperatures , ptrm_checks_starting_temperatures , x_ptrm_check , y_ptrm_check , tail_checks_temperatures , tail_checks_starting_temperatures , x_tail_check , y_tail_check ) :
"""returns relevant points for a SCAT test""" | points = [ ]
points_arai = [ ]
points_ptrm = [ ]
points_tail = [ ]
for i in range ( len ( x_Arai_segment ) ) : # uses only the best _ fit segment , so no need for further selection
x = x_Arai_segment [ i ]
y = y_Arai_segment [ i ]
points . append ( ( x , y ) )
points_arai . append ( ( x , y ) )
for num ... |
def _new_initial_request ( self , with_body : bool = True ) :
'''Return a new Request to be passed to the Web Client .''' | url_record = self . _item_session . url_record
url_info = url_record . url_info
request = self . _item_session . app_session . factory [ 'WebClient' ] . request_factory ( url_info . url )
self . _populate_common_request ( request )
if with_body :
if url_record . post_data or self . _processor . fetch_params . post_... |
def two_point_attempts ( self ) :
"""Returns an ` ` int ` ` of the total number of two point field goals the
player attempted during the season .""" | if self . field_goal_attempts and self . three_point_attempts :
return int ( self . field_goal_attempts - self . three_point_attempts )
# Occurs when the player didn ' t take any three pointers , so the number
# of two pointers the player took is equal to the total number of field
# goals the player took .
if self ... |
def boundary_stawiaski ( graph , label_image , gradient_image ) : # label image is not required to hold continuous ids or to start from 1
r"""Boundary term based on the sum of border voxel pairs differences .
An implementation of the boundary term in [ 1 ] _ , suitable to be used with the ` ~ medpy . graphcut . g... | # convert to arrays if necessary
label_image = scipy . asarray ( label_image )
gradient_image = scipy . asarray ( gradient_image )
if label_image . flags [ 'F_CONTIGUOUS' ] : # strangely , this one is required to be ctype ordering
label_image = scipy . ascontiguousarray ( label_image )
__check_label_image ( label_i... |
def bowtie ( self ) :
"""Create threads and commands for performing reference mapping for qualimap analyses""" | for i in range ( self . cpus ) : # Send the threads to the merge method . : args is empty as I ' m using
threads = Thread ( target = self . align , args = ( ) )
# Set the daemon to true - something to do with thread management
threads . setDaemon ( True )
# Start the threading
threads . start ( )
wi... |
def multi_future ( children , quiet_exceptions = ( ) ) :
"""Wait for multiple asynchronous futures in parallel .
This function is similar to ` multi ` , but does not support
` YieldPoints < YieldPoint > ` .
. . versionadded : : 4.0
. . versionchanged : : 4.2
If multiple ` ` Futures ` ` fail , any exceptio... | if isinstance ( children , dict ) :
keys = list ( children . keys ( ) )
children = children . values ( )
else :
keys = None
children = list ( map ( convert_yielded , children ) )
assert all ( is_future ( i ) for i in children )
unfinished_children = set ( children )
future = Future ( )
if not children :
... |
def applyFilter ( normalized_uri , xrd_data , flt = None ) :
"""Generate an iterable of endpoint objects given this input data ,
presumably from the result of performing the Yadis protocol .
@ param normalized _ uri : The input URL , after following redirects ,
as in the Yadis protocol .
@ param xrd _ data ... | flt = mkFilter ( flt )
et = parseXRDS ( xrd_data )
endpoints = [ ]
for service_element in iterServices ( et ) :
endpoints . extend ( flt . getServiceEndpoints ( normalized_uri , service_element ) )
return endpoints |
def list_files ( tag = '' , sat_id = None , data_path = None , format_str = None ) :
"""Return a Pandas Series of every file for chosen satellite data
Parameters
tag : ( string or NoneType )
Denotes type of file to load . Accepted types are ' ' and ' ascii ' .
If ' ' is specified , the primary data type ( a... | if format_str is None and tag is not None :
if tag == '' or tag == 'ascii' :
ascii_fmt = 'Density_3deg_{year:02d}_{doy:03d}.ascii'
return pysat . Files . from_os ( data_path = data_path , format_str = ascii_fmt )
else :
raise ValueError ( 'Unrecognized tag name for CHAMP STAR' )
elif for... |
def set_field ( self , state , field_name , field_type , value ) :
"""Sets an instance field .""" | field_ref = SimSootValue_InstanceFieldRef . get_ref ( state = state , obj_alloc_id = self . heap_alloc_id , field_class_name = self . type , field_name = field_name , field_type = field_type )
# store value in java memory
state . memory . store ( field_ref , value ) |
def i2m ( self , pkt , i ) :
"""" Internal " ( IP as bytes , mask as int ) to " machine " representation .""" | # noqa : E501
mask , ip = i
ip = pton_ntop . inet_pton ( socket . AF_INET6 , ip )
return struct . pack ( ">B" , mask ) + ip [ : self . mask2iplen ( mask ) ] |
def read_plain_boolean ( file_obj , count ) :
"""Read ` count ` booleans using the plain encoding .""" | # for bit packed , the count is stored shifted up . But we want to pass in a count ,
# so we shift up .
# bit width is 1 for a single - bit boolean .
return read_bitpacked ( file_obj , count << 1 , 1 , logger . isEnabledFor ( logging . DEBUG ) ) |
def reset ( self ) :
"""Clears all entries .
: return : None""" | for i in range ( len ( self . values ) ) :
self . values [ i ] . delete ( 0 , tk . END )
if self . defaults [ i ] is not None :
self . values [ i ] . insert ( 0 , self . defaults [ i ] ) |
def get_stories ( self , * args , ** kwargs ) :
"""Fetches lists of stories .
get / v1 / public / stories
: returns : StoryDataWrapper
> > > # Find all the stories that involved both Hulk and Wolverine
> > > # hulk ' s id : 1009351
> > > # wolverine ' s id : 1009718
> > > m = Marvel ( public _ key , pri... | response = json . loads ( self . _call ( Story . resource_url ( ) , self . _params ( kwargs ) ) . text )
return StoryDataWrapper ( self , response ) |
def get ( self , * args , ** kwargs ) :
"""Perform a get request .""" | if 'convert' in kwargs :
conversion = kwargs . pop ( 'convert' )
else :
conversion = True
kwargs = self . _get_keywords ( ** kwargs )
url = self . _create_path ( * args )
request = self . session . get ( url , params = kwargs )
content = request . content
self . _request = request
return self . convert ( conten... |
def _recv_keys ( self , keyids , keyserver = None ) :
"""Import keys from a keyserver .
: param str keyids : A space - delimited string containing the keyids to
request .
: param str keyserver : The keyserver to request the ` ` keyids ` ` from ;
defaults to ` gnupg . GPG . keyserver ` .""" | if not keyserver :
keyserver = self . keyserver
args = [ '--keyserver {0}' . format ( keyserver ) , '--recv-keys {0}' . format ( keyids ) ]
log . info ( 'Requesting keys from %s: %s' % ( keyserver , keyids ) )
result = self . _result_map [ 'import' ] ( self )
proc = self . _open_subprocess ( args )
self . _collect_... |
def _group ( self , obj , val , behavior ) :
"""An internal function used for aggregate " group by " operations .""" | ns = self . Namespace ( )
ns . result = { }
iterator = self . _lookupIterator ( val )
def e ( value , index , * args ) :
key = iterator ( value , index )
behavior ( ns . result , key , value )
_ . each ( obj , e )
if len ( ns . result ) == 1 :
try :
return ns . result [ 0 ]
except KeyError :
... |
def getLayerIndex ( self , layer ) :
"""Given a reference to a layer , returns the index of that layer in
self . layers .""" | for i in range ( len ( self . layers ) ) :
if layer == self . layers [ i ] : # shallow cmp
return i
return - 1
# not in list |
def by_pdb ( self , pdb_id , take_top_percentile = 30.0 , cut_off = None , matrix = None , sequence_identity_cut_off = None , silent = None ) :
'''Returns a list of all PDB files which contain protein sequences similar to the protein sequences of pdb _ id .
Only protein chains are considered in the matching so e ... | self . log ( 'BLASTing {0}' . format ( pdb_id ) , silent , colortext . pcyan )
# Preamble
matrix = matrix or self . matrix
cut_off = cut_off or self . cut_off
sequence_identity_cut_off = sequence_identity_cut_off or self . sequence_identity_cut_off
# Parse PDB file
p = self . bio_cache . get_pdb_object ( pdb_id )
chain... |
def set_level ( self , level = 1 ) :
"""Set the logging level
Parameters
level : ` int ` or ` bool ` ( optional , default : 1)
If False or 0 , prints WARNING and higher messages .
If True or 1 , prints INFO and higher messages .
If 2 or higher , prints all messages .""" | if level is True or level == 1 :
level = logging . INFO
level_name = "INFO"
elif level is False or level <= 0 :
level = logging . WARNING
level_name = "WARNING"
elif level >= 2 :
level = logging . DEBUG
level_name = "DEBUG"
if not self . logger . handlers :
self . logger . tasklogger = self
... |
def _set_ca ( self , v , load = False ) :
"""Setter method for ca , mapped from YANG variable / rbridge _ id / crypto / ca ( list )
If this variable is read - only ( config : false ) in the
source YANG file , then _ set _ ca is considered as a private
method . Backends looking to populate this variable should... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = YANGListType ( "trustpoint" , ca . ca , yang_name = "ca" , rest_name = "ca" , parent = self , is_container = 'list' , user_ordered = False , path_helper = self . _path_helper , yang_keys = 'trustpoint' , extensions = { u'tail... |
def get_sequence_rule_lookup_session_for_bank ( self , bank_id , proxy ) :
"""Gets the ` ` OsidSession ` ` associated with the sequence rule lookup service for the given bank .
arg : bank _ id ( osid . id . Id ) : the ` ` Id ` ` of the ` ` Bank ` `
arg : proxy ( osid . proxy . Proxy ) : a proxy
return : ( osi... | if not self . supports_sequence_rule_lookup ( ) :
raise errors . Unimplemented ( )
# Also include check to see if the catalog Id is found otherwise raise errors . NotFound
# pylint : disable = no - member
return sessions . SequenceRuleLookupSession ( bank_id , proxy , self . _runtime ) |
def shot_chart_jointplot ( x , y , data = None , kind = "scatter" , title = "" , color = "b" , cmap = None , xlim = ( - 250 , 250 ) , ylim = ( 422.5 , - 47.5 ) , court_color = "gray" , court_lw = 1 , outer_lines = False , flip_court = False , size = ( 12 , 11 ) , space = 0 , despine = False , joint_kws = None , margina... | # If a colormap is not provided , then it is based off of the color
if cmap is None :
cmap = sns . light_palette ( color , as_cmap = True )
if kind not in [ "scatter" , "kde" , "hex" ] :
raise ValueError ( "kind must be 'scatter', 'kde', or 'hex'." )
grid = sns . jointplot ( x = x , y = y , data = data , stat_f... |
def list_ifd ( self ) :
"""Return the list of IFDs in the header .""" | i = self . _first_ifd ( )
ifds = [ ]
while i :
ifds . append ( i )
i = self . _next_ifd ( i )
return ifds |
def regex_check ( equation_str ) :
"""A quick regular expression check to see that the input is sane
Args :
equation _ str ( str ) : String of equation to be parsed by sympify
function . Expected to be valid Python .
Raises :
BadInputError : If input does not look safe to parse as an equation .""" | match1 = re . match ( r'^(([xy+\-*/()0-9. ]+|sin\(|cos\(|exp\(|log\()?)+$' , equation_str )
match2 = re . match ( r'^.*([xy]) *([xy]).*$' , equation_str )
if match1 and not match2 :
return True
raise BadInputError ( 'Cannot parse entered equation' ) |
def get_information ( self ) :
"""Return information about the connected bank .
Note : Can only be filled after the first communication with the bank .
If in doubt , use a construction like : :
f = FinTS3Client ( . . . )
with f :
info = f . get _ information ( )
Returns a nested dictionary : :
bank : ... | retval = { 'bank' : { } , 'accounts' : [ ] , 'auth' : { } , }
if self . bpa :
retval [ 'bank' ] [ 'name' ] = self . bpa . bank_name
if self . bpd . segments :
retval [ 'bank' ] [ 'supported_operations' ] = { op : any ( self . bpd . find_segment_first ( cmd [ 0 ] + 'I' + cmd [ 2 : ] + 'S' ) for cmd in op . value... |
def do_hdr ( self , line , hdrs_usr ) :
"""Initialize self . h2i .""" | # If there is no header hint , consider the first line the header .
if self . hdr_ex is None :
self . _init_hdr ( line , hdrs_usr )
return True
# If there is a header hint , examine each beginning line until header hint is found .
elif self . hdr_ex in line :
self . _init_hdr ( line , hdrs_usr )
return ... |
def router_fabric_virtual_gateway_address_family_ipv4_gratuitous_arp_timer ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
router = ET . SubElement ( config , "router" , xmlns = "urn:brocade.com:mgmt:brocade-common-def" )
fabric_virtual_gateway = ET . SubElement ( router , "fabric-virtual-gateway" , xmlns = "urn:brocade.com:mgmt:brocade-anycast-gateway" )
address_family = ET . SubElement ( fabric_virtual_... |
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