signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def postinit ( self , items = None , body = None , type_annotation = None ) :
"""Do some setup after initialisation .
: param items : The pairs of context managers and the names
they are assigned to .
: type items : list ( tuple ( NodeNG , AssignName or None ) ) or None
: param body : The contents of the ` ... | self . items = items
self . body = body
self . type_annotation = type_annotation |
def get_jids ( ) :
'''Return a list of all job ids''' | serv = _get_serv ( ret = None )
sql = "select distinct(jid) from jids group by load"
# [ { u ' points ' : [ [ 0 , jid , load ] ,
# [0 , jid , load ] ] ,
# u ' name ' : u ' jids ' ,
# u ' columns ' : [ u ' time ' , u ' distinct ' , u ' load ' ] } ]
data = serv . query ( sql )
ret = { }
if data :
for _ , jid , load i... |
def set_last_component_continued ( self ) : # type : ( ) - > None
'''Set the previous component of this SL record to continued .
Parameters :
None .
Returns :
Nothing .''' | if not self . _initialized :
raise pycdlibexception . PyCdlibInternalError ( 'SL record not yet initialized!' )
if not self . symlink_components :
raise pycdlibexception . PyCdlibInternalError ( 'Trying to set continued on a non-existent component!' )
self . symlink_components [ - 1 ] . set_continued ( ) |
def _CreateFolder ( self , parent , name , visible = True , description = None ) :
"""Create a KML Folder element .
Args :
parent : The parent ElementTree . Element instance .
name : The folder name as a string .
visible : Whether the folder is initially visible or not .
description : A description string... | folder = ET . SubElement ( parent , 'Folder' )
name_tag = ET . SubElement ( folder , 'name' )
name_tag . text = name
if description is not None :
desc_tag = ET . SubElement ( folder , 'description' )
desc_tag . text = description
if not visible :
visibility = ET . SubElement ( folder , 'visibility' )
vi... |
def _connection_parameters ( self ) :
"""Return connection parameters for a pika connection .
: rtype : pika . ConnectionParameters""" | return pika . ConnectionParameters ( self . config . get ( 'host' , 'localhost' ) , self . config . get ( 'port' , 5672 ) , self . config . get ( 'vhost' , '/' ) , pika . PlainCredentials ( self . config . get ( 'user' , 'guest' ) , self . config . get ( 'password' , self . config . get ( 'pass' , 'guest' ) ) ) , ssl =... |
def _get_hover_data ( self , data , element ) :
"""Initializes hover data based on Element dimension values .""" | if 'hover' not in self . handles or self . static_source :
return
for k , v in self . overlay_dims . items ( ) :
dim = util . dimension_sanitizer ( k . name )
if dim not in data :
data [ dim ] = [ v for _ in range ( len ( list ( data . values ( ) ) [ 0 ] ) ) ] |
def create_payload ( self ) :
"""Wrap submitted data within an extra dict .
For more information , see ` Bugzilla # 1151220
< https : / / bugzilla . redhat . com / show _ bug . cgi ? id = 1151220 > ` _ .""" | payload = super ( ConfigTemplate , self ) . create_payload ( )
if 'template_combinations' in payload :
payload [ 'template_combinations_attributes' ] = payload . pop ( 'template_combinations' )
return { u'config_template' : payload } |
def deltet ( epoch , eptype ) :
"""Return the value of Delta ET ( ET - UTC ) for an input epoch .
http : / / naif . jpl . nasa . gov / pub / naif / toolkit _ docs / C / cspice / deltet _ c . html
: param epoch : Input epoch ( seconds past J2000 ) .
: type epoch : float
: param eptype : Type of input epoch (... | epoch = ctypes . c_double ( epoch )
eptype = stypes . stringToCharP ( eptype )
delta = ctypes . c_double ( )
libspice . deltet_c ( epoch , eptype , ctypes . byref ( delta ) )
return delta . value |
def _clean_html ( html ) :
"""Removes links ( ` ` < a href = " . . . " > . . . < / a > ` ` ) from the provided HTML input .
Further , it replaces " & # x000A ; " with ` ` \n ` ` and removes " ¶ " from the texts .""" | content = html . replace ( u'
' , u'\n' ) . replace ( u'¶' , '' )
content = _LINK_PATTERN . sub ( u'' , content )
content = _HTML_TAG_PATTERN . sub ( u'' , content )
content = _BACKSLASH_PATTERN . sub ( u'\n' , content )
return content |
def _render_content ( self , content , ** settings ) :
"""Perform widget rendering , but do not print anything .""" | if not self . SETTING_WIDTH in settings or not settings [ self . SETTING_WIDTH ] :
settings [ self . SETTING_WIDTH ] = TERMINAL_WIDTH
s = { k : settings [ k ] for k in ( self . SETTING_WIDTH , self . SETTING_FLAG_BORDER , self . SETTING_MARGIN , self . SETTING_MARGIN_LEFT , self . SETTING_MARGIN_RIGHT , self . SETT... |
def gpg_list_profile_keys ( blockchain_id , proxy = None , wallet_keys = None , config_dir = None ) :
"""List all GPG keys in a user profile :
Return a list of { ' identifier ' : key ID , ' contentUrl ' : URL to the key data } on success
Raise on error
Return { ' error ' : . . . } on failure""" | config_dir = get_config_dir ( config_dir )
client_config_path = os . path . join ( config_dir , blockstack_client . CONFIG_FILENAME )
if proxy is None :
proxy = blockstack_client . get_default_proxy ( config_path = client_config_path )
accounts = blockstack_client . list_accounts ( blockchain_id , proxy = proxy )
i... |
def partition ( self , ref = None , ** kwargs ) :
"""Return a partition in this bundle for a vid reference or name parts""" | from ambry . orm . exc import NotFoundError
from sqlalchemy . orm . exc import NoResultFound
if not ref and not kwargs :
return None
if ref :
for p in self . partitions :
if ref == p . name or ref == p . vname or ref == p . vid or ref == p . id :
p . _bundle = self
return p
r... |
def ports ( self ) :
'''The list of all ports belonging to this component .''' | with self . _mutex :
if not self . _ports :
self . _ports = [ ports . parse_port ( port , self ) for port in self . _obj . get_ports ( ) ]
return self . _ports |
def residual_unit ( data , num_filter , stride , dim_match , name , bottle_neck = True , num_group = 32 , bn_mom = 0.9 , workspace = 256 , memonger = False ) :
"""Return ResNet Unit symbol for building ResNet
Parameters
data : str
Input data
num _ filter : int
Number of output channels
bnf : int
Bottl... | if bottle_neck : # the same as https : / / github . com / facebook / fb . resnet . torch # notes , a bit difference with origin paper
conv1 = mx . sym . Convolution ( data = data , num_filter = int ( num_filter * 0.5 ) , kernel = ( 1 , 1 ) , stride = ( 1 , 1 ) , pad = ( 0 , 0 ) , no_bias = True , workspace = worksp... |
def _get_esxdatacenter_proxy_details ( ) :
'''Returns the running esxdatacenter ' s proxy details''' | det = __salt__ [ 'esxdatacenter.get_details' ] ( )
return det . get ( 'vcenter' ) , det . get ( 'username' ) , det . get ( 'password' ) , det . get ( 'protocol' ) , det . get ( 'port' ) , det . get ( 'mechanism' ) , det . get ( 'principal' ) , det . get ( 'domain' ) , det . get ( 'datacenter' ) |
def hash_file_contents ( requirements_option : RequirementsOptions , path : Path ) -> str :
"""Returns a SHA256 hash of the contents of ` ` path ` ` combined with the Arca version .""" | return hashlib . sha256 ( path . read_bytes ( ) + bytes ( requirements_option . name + arca . __version__ , "utf-8" ) ) . hexdigest ( ) |
def cn_occupation_energy ( self , delta_occupation = None ) :
"""The coordination - number dependent energy for this site .
Args :
delta _ occupation ( : obj : Dict ( Str : Int ) , optional ) : A dictionary of a change in ( site - type specific ) coordination number , e . g . { ' A ' : 1 , ' B ' : - 1 } .
If ... | nn_occupations = self . site_specific_nn_occupation ( )
if delta_occupation :
for site in delta_occupation :
assert ( site in nn_occupations )
nn_occupations [ site ] += delta_occupation [ site ]
return sum ( [ self . cn_occupation_energies [ s ] [ n ] for s , n in nn_occupations . items ( ) ] ) |
def _dump_linestring ( obj , big_endian , meta ) :
"""Dump a GeoJSON - like ` dict ` to a linestring WKB string .
Input parameters and output are similar to : func : ` _ dump _ point ` .""" | coords = obj [ 'coordinates' ]
vertex = coords [ 0 ]
# Infer the number of dimensions from the first vertex
num_dims = len ( vertex )
wkb_string , byte_fmt , byte_order = _header_bytefmt_byteorder ( 'LineString' , num_dims , big_endian , meta )
# append number of vertices in linestring
wkb_string += struct . pack ( '%s... |
def total_amount ( qs ) -> Total :
"""Sums the amounts of the objects in the queryset , keeping each currency separate .
: param qs : A querystring containing objects that have an amount field of type Money .
: return : A Total object .""" | aggregate = qs . values ( 'amount_currency' ) . annotate ( sum = Sum ( 'amount' ) )
return Total ( Money ( amount = r [ 'sum' ] , currency = r [ 'amount_currency' ] ) for r in aggregate ) |
def _sprite ( map , sprite , offset_x = None , offset_y = None ) :
"""Returns the image and background position for use in a single shorthand
property""" | map = StringValue ( map ) . value
sprite_name = StringValue ( sprite ) . value
sprite_map = sprite_maps . get ( map )
sprite = sprite_map and sprite_map . get ( sprite_name )
if not sprite_map :
log . error ( "No sprite map found: %s" , map )
elif not sprite :
log . error ( "No sprite found: %s in %s" , sprite_... |
def get_closest_match ( self , motifs , dbmotifs = None , match = "partial" , metric = "wic" , combine = "mean" , parallel = True , ncpus = None ) :
"""Return best match in database for motifs .
Parameters
motifs : list or str
Filename of motifs or list of motifs .
dbmotifs : list or str , optional
Databa... | if dbmotifs is None :
pwm = self . config . get_default_params ( ) [ "motif_db" ]
pwmdir = self . config . get_motif_dir ( )
dbmotifs = os . path . join ( pwmdir , pwm )
motifs = parse_motifs ( motifs )
dbmotifs = parse_motifs ( dbmotifs )
dbmotif_lookup = dict ( [ ( m . id , m ) for m in dbmotifs ] )
score... |
def run ( self ) :
"""Main entrypoint method .
Returns
new _ nodes : ` list `
Nodes to add to the doctree .""" | if getLogger is not None : # Sphinx 1.6 +
logger = getLogger ( __name__ )
else : # Previously Sphinx ' s app was also the logger
logger = self . state . document . settings . env . app
env = self . state . document . settings . env
new_nodes = [ ]
# Get skip list
skipped_modules = self . _parse_skip_option ( )
... |
def export_users ( self , body ) :
"""Export all users to a file using a long running job .
Check job status with get ( ) . URL pointing to the export file will be
included in the status once the job is complete .
Args :
body ( dict ) : Please see : https : / / auth0 . com / docs / api / management / v2 # !... | return self . client . post ( self . _url ( 'users-exports' ) , data = body ) |
def read_files ( * sources , ** kwds ) :
"""Construct a generator that yields file instances .
: param sources : One or more strings representing path to file ( s ) .""" | filenames = _generate_filenames ( sources )
filehandles = _generate_handles ( filenames )
for fh , source in filehandles :
try :
f = mwtab . MWTabFile ( source )
f . read ( fh )
if kwds . get ( 'validate' ) :
validator . validate_file ( mwtabfile = f , section_schema_mapping = mw... |
def _alerter_thread_func ( self ) -> None :
"""Prints alerts and updates the prompt any time the prompt is showing""" | self . _alert_count = 0
self . _next_alert_time = 0
while not self . _stop_thread : # Always acquire terminal _ lock before printing alerts or updating the prompt
# To keep the app responsive , do not block on this call
if self . terminal_lock . acquire ( blocking = False ) : # Get any alerts that need to be printe... |
def execute_command ( self ) :
"""The generate command uses ` Jinja2 < http : / / jinja . pocoo . org / > ` _ templates to create Python scripts , according to the specification in the configuration file . The predefined templates use the extract _ content ( ) method of the : ref : ` selector classes < implementati... | print ( Back . GREEN + Fore . BLACK + "Scrapple Generate" )
print ( Back . RESET + Fore . RESET )
directory = os . path . join ( scrapple . __path__ [ 0 ] , 'templates' , 'scripts' )
with open ( os . path . join ( directory , 'generate.txt' ) , 'r' ) as f :
template_content = f . read ( )
template = Template ( temp... |
def remove ( self , key , preserve_data = False ) :
""": param key : Document unique identifier .
Remove the document from the search index .""" | if self . members . remove ( key ) != 1 :
raise KeyError ( 'Document with key "%s" not found.' % key )
document_hash = self . _get_hash ( key )
content = decode ( document_hash [ 'content' ] )
if not preserve_data :
document_hash . clear ( )
for word in self . tokenizer . tokenize ( content ) :
word_key = s... |
def system_find_databases ( input_params = { } , always_retry = True , ** kwargs ) :
"""Invokes the / system / findDatabases API method .
For more info , see : https : / / wiki . dnanexus . com / API - Specification - v1.0.0 / Search # API - method % 3A - % 2Fsystem % 2FfindDatabases""" | return DXHTTPRequest ( '/system/findDatabases' , input_params , always_retry = always_retry , ** kwargs ) |
def unwrapArray ( a , recursive = True , readH5pyDataset = True ) :
"""This function takes an object ( like a dictionary ) and recursively
unwraps it solving issues like :
* the fact that many objects are packaged as 0d array
This funciton has also some specific hack for handling h5py limits :
* handle the ... | try : # # # take care of hdf5 groups
if isinstance ( a , h5py . Group ) : # take care of special flags first
if isinstance ( a , h5py . Group ) and ( ( "IS_LIST" in a . attrs ) or ( "IS_LIST_OF_ARRAYS" in a . attrs ) ) :
items = list ( a . keys ( ) )
items . sort ( )
a = ... |
def _ReadCompressedData ( self , read_size ) :
"""Reads compressed data from the file - like object .
Args :
read _ size ( int ) : number of bytes of compressed data to read .
Returns :
int : number of bytes of compressed data read .""" | compressed_data = self . _file_object . read ( read_size )
read_count = len ( compressed_data )
self . _compressed_data = b'' . join ( [ self . _compressed_data , compressed_data ] )
self . _uncompressed_data , self . _compressed_data = ( self . _decompressor . Decompress ( self . _compressed_data ) )
self . _uncompres... |
def caesar_app ( parser , cmd , args ) : # pragma : no cover
"""Caesar crypt a value with a key .""" | parser . add_argument ( 'shift' , type = int , help = 'the shift to apply' )
parser . add_argument ( 'value' , help = 'the value to caesar crypt, read from stdin if omitted' , nargs = '?' )
parser . add_argument ( '-s' , '--shift-range' , dest = 'shift_ranges' , action = 'append' , help = 'specify a character range to ... |
def group_protocols ( self ) :
"""Returns list of preferred ( protocols , metadata )""" | if self . _subscription . subscription is None :
raise Errors . IllegalStateError ( 'Consumer has not subscribed to topics' )
# dpkp note : I really dislike this .
# why ? because we are using this strange method group _ protocols ,
# which is seemingly innocuous , to set internal state ( _ joined _ subscription )
... |
def p_delays_intnumber ( self , p ) :
'delays : DELAY intnumber' | p [ 0 ] = DelayStatement ( IntConst ( p [ 2 ] , lineno = p . lineno ( 1 ) ) , lineno = p . lineno ( 1 ) )
p . set_lineno ( 0 , p . lineno ( 1 ) ) |
def get_column_flat ( self , field , components = None , computed_type = 'for_observations' ) :
"""TODO : add documentation
return a single merged value ( hstacked ) from all meshes
: parameter str field : name of the mesh columnname
: parameter components :""" | return self . pack_column_flat ( self . get_column ( field , components , computed_type ) , components , offset = field == 'triangles' ) |
def make_response ( self , rv , status = 200 , headers = None , mime = 'application/json' ) :
"""Create a response object using the : class : ` flask . Response ` class .
: param rv : Response value . If the value is not an instance
of : class : ` werkzeug . wrappers . Response ` it will be converted
into a R... | if not isinstance ( rv , Response ) :
resp = Response ( response = rv , headers = headers , mimetype = mime , status = status )
else :
resp = rv
return resp |
def has_shared ( arg , shared ) :
"""Verifica se ci sono shared .""" | try :
if isinstance ( shared , list ) :
shared_arguments = shared
else :
shared_arguments = shared . __shared_arguments__
for idx , ( args , kwargs ) in enumerate ( shared_arguments ) :
arg_name = kwargs . get ( 'dest' , args [ - 1 ] . lstrip ( '-' ) . replace ( '-' , '_' ) )
... |
def parse_delta ( filename ) :
"""Returns ( alignment length , similarity errors ) tuple from passed . delta .
- filename - path to the input . delta file
Extracts the aligned length and number of similarity errors for each
aligned uniquely - matched region , and returns the cumulative total for
each as a t... | aln_length , sim_errors = 0 , 0
for line in [ l . strip ( ) . split ( ) for l in open ( filename , "r" ) . readlines ( ) ] :
if line [ 0 ] == "NUCMER" or line [ 0 ] . startswith ( ">" ) : # Skip headers
continue
# We only process lines with seven columns :
if len ( line ) == 7 :
aln_length +... |
def _split_diff ( merge_result , context_lines = 3 ) :
"""Split diffs and context lines into groups based on None sentinel""" | collect = [ ]
for item in _visible_in_diff ( merge_result , context_lines = context_lines ) :
if item is None :
if collect :
yield collect
collect = [ ]
else :
collect . append ( item ) |
def construct_surface ( direction , * args , ** kwargs ) :
"""Generates surfaces from curves .
Arguments :
* ` ` args ` ` : a list of curve instances
Keyword Arguments ( optional ) :
* ` ` degree ` ` : degree of the 2nd parametric direction
* ` ` knotvector ` ` : knot vector of the 2nd parametric directio... | # Input validation
possible_dirs = [ 'u' , 'v' ]
if direction not in possible_dirs :
raise GeomdlException ( "Possible direction values: " + ", " . join ( [ val for val in possible_dirs ] ) , data = dict ( input_dir = direction ) )
size_other = len ( args )
if size_other < 2 :
raise GeomdlException ( "You need ... |
def plot ( self , win = None , newfig = True , figsize = None , orientation = 'hor' , topfigfrac = 0.8 ) :
"""Plot layout
Parameters
win : list or tuple
[ x1 , x2 , y1 , y2]""" | if newfig :
plt . figure ( figsize = figsize )
ax1 = None
ax2 = None
if orientation == 'both' :
ax1 = plt . axes ( [ 0.125 , 0.18 + ( 1 - topfigfrac ) * 0.7 , ( 0.9 - 0.125 ) , topfigfrac * 0.7 ] )
ax2 = plt . axes ( [ 0.125 , 0.11 , ( 0.9 - 0.125 ) , ( 1 - topfigfrac ) * 0.7 ] , sharex ... |
def load_parameters ( self , source ) :
"""For YML , the source it the file path""" | with open ( source ) as parameters_source :
loaded = yaml . safe_load ( parameters_source . read ( ) )
for k , v in loaded . items ( ) :
if isinstance ( v , str ) :
loaded [ k ] = "'" + v + "'"
return loaded |
def AddStopObject ( self , stop , problem_reporter = None ) :
"""Add Stop object to this schedule if stop _ id is non - blank .""" | assert stop . _schedule is None
if not problem_reporter :
problem_reporter = self . problem_reporter
if not stop . stop_id :
return
if stop . stop_id in self . stops :
problem_reporter . DuplicateID ( 'stop_id' , stop . stop_id )
return
stop . _schedule = weakref . proxy ( self )
self . AddTableColumns ... |
def main ( self ) -> None :
"""Main entry point . Runs : func : ` service ` .""" | # Actual main service code .
try :
self . service ( )
except Exception as e :
self . error ( "Unexpected exception: {e}\n{t}" . format ( e = e , t = traceback . format_exc ( ) ) ) |
def get_identities ( self , item ) :
"""Return the identities from an item""" | # All identities are in the post stream
# The first post is the question . Next replies
posts = item [ 'data' ] [ 'post_stream' ] [ 'posts' ]
for post in posts :
user = self . get_sh_identity ( post )
yield user |
def bind ( self , context ) -> None :
"""Bind a context to this computation .
The context allows the computation to convert object specifiers to actual objects .""" | # make a computation context based on the enclosing context .
self . __computation_context = ComputationContext ( self , context )
# re - bind is not valid . be careful to set the computation after the data item is already in document .
for variable in self . variables :
assert variable . bound_item is None
for res... |
def environment_list ( self , io_handler ) :
"""Lists the framework process environment variables""" | # Head of the table
headers = ( "Environment Variable" , "Value" )
# Lines
lines = [ item for item in os . environ . items ( ) ]
# Sort lines
lines . sort ( )
# Print the table
io_handler . write ( self . _utils . make_table ( headers , lines ) ) |
def see_tooltip ( step , tooltip ) :
"""Press a button having a given tooltip .""" | elem = world . browser . find_elements_by_xpath ( str ( '//*[@title="%(tooltip)s" or @data-original-title="%(tooltip)s"]' % dict ( tooltip = tooltip ) ) )
elem = [ e for e in elem if e . is_displayed ( ) ]
assert_true ( step , elem ) |
def flagants ( self , threshold = 50 ) :
"""Flags solutions with amplitude more than threshold larger than median .""" | # identify very low gain amps not already flagged
badsols = n . where ( ( n . median ( self . amp ) / self . amp > threshold ) & ( self . flagged == False ) ) [ 0 ]
if len ( badsols ) :
self . logger . info ( 'Solutions %s flagged (times %s, ants %s, freqs %s) for low gain amplitude.' % ( str ( badsols ) , self . m... |
def get ( self , deviceId ) :
"""lists all known active measurements .""" | measurementsByName = self . measurements . get ( deviceId )
if measurementsByName is None :
return [ ]
else :
return list ( measurementsByName . values ( ) ) |
def theme ( self , text ) :
'''Theme style .''' | return self . theme_color + self . BRIGHT + text + self . RESET |
def _interpretPayload ( functioncode , payload ) :
r"""Generate a human readable description of a Modbus payload .
Args :
* functioncode ( int ) : Function code
* payload ( str ) : The payload that should be interpreted . It should be a byte string .
Returns :
A descriptive string .
For example , the pa... | raise NotImplementedError ( )
output = ''
output += 'Modbus payload decoder\n'
output += 'Input payload (length {} characters): {!r} \n' . format ( len ( payload ) , payload )
output += 'Function code: {} (dec).\n' . format ( functioncode )
if len ( payload ) == 4 :
FourbyteMessageFirstHalfValue = _twoByteStringToN... |
def _autofill_spec_record ( record ) :
"""Returns an astropy table with columns auto - filled from FITS header
Parameters
record : astropy . io . fits . table . table . Row
The spectrum table row to scrape
Returns
record : astropy . io . fits . table . table . Row
The spectrum table row with possible ne... | try :
record [ 'filename' ] = os . path . basename ( record [ 'spectrum' ] )
if record [ 'spectrum' ] . endswith ( '.fits' ) :
header = pf . getheader ( record [ 'spectrum' ] )
# Wavelength units
if not record [ 'wavelength_units' ] :
try :
record [ 'wavelengt... |
def _api_config ( self ) :
"""Glances API RESTful implementation .
Return the JSON representation of the Glances configuration file
HTTP / 200 if OK
HTTP / 404 if others error""" | response . content_type = 'application/json; charset=utf-8'
try : # Get the JSON value of the config ' dict
args_json = json . dumps ( self . config . as_dict ( ) )
except Exception as e :
abort ( 404 , "Cannot get config (%s)" % str ( e ) )
return args_json |
def Rzderiv ( self , R , Z , phi = 0. , t = 0. ) :
"""NAME :
Rzderiv
PURPOSE :
evaluate the mixed R , z derivative
INPUT :
R - Galactocentric radius ( can be Quantity )
Z - vertical height ( can be Quantity )
phi - Galactocentric azimuth ( can be Quantity )
t - time ( can be Quantity )
OUTPUT :
... | try :
return self . _amp * self . _Rzderiv ( R , Z , phi = phi , t = t )
except AttributeError : # pragma : no cover
raise PotentialError ( "'_Rzderiv' function not implemented for this potential" ) |
def query ( self , coords , ** kwargs ) :
"""Returns E ( B - V ) ( or a different Planck dust inference , depending on how
the class was intialized ) at the specified location ( s ) on the sky .
Args :
coords ( : obj : ` astropy . coordinates . SkyCoord ` ) : The coordinates to query .
Returns :
A float a... | return self . _scale * super ( PlanckQuery , self ) . query ( coords , ** kwargs ) |
def find ( self , text ) :
"""Print all substitutions that include the given text string .""" | for key , value in self :
if ( text in key ) or ( text in value ) :
print ( key , value ) |
def star ( args ) :
"""% prog star folder reference
Run star on a folder with reads .""" | p = OptionParser ( star . __doc__ )
p . add_option ( "--single" , default = False , action = "store_true" , help = "Single end mapping" )
p . set_fastq_names ( )
p . set_cpus ( )
opts , args = p . parse_args ( args )
if len ( args ) != 2 :
sys . exit ( not p . print_help ( ) )
folder , reference = args
cpus = opts ... |
def json_compat_obj_encode ( data_type , obj , caller_permissions = None , alias_validators = None , old_style = False , for_msgpack = False , should_redact = False ) :
"""Encodes an object into a JSON - compatible dict based on its type .
Args :
data _ type ( Validator ) : Validator for obj .
obj ( object ) ... | serializer = StoneToPythonPrimitiveSerializer ( caller_permissions , alias_validators , for_msgpack , old_style , should_redact )
return serializer . encode ( data_type , obj ) |
def _find_cont_fitfunc_regions ( fluxes , ivars , contmask , deg , ranges , ffunc , n_proc = 1 ) :
"""Run fit _ cont , dealing with spectrum in regions or chunks
This is useful if a spectrum has gaps .
Parameters
fluxes : ndarray of shape ( nstars , npixels )
training set or test set pixel intensities
iva... | nstars = fluxes . shape [ 0 ]
npixels = fluxes . shape [ 1 ]
cont = np . zeros ( fluxes . shape )
for chunk in ranges :
start = chunk [ 0 ]
stop = chunk [ 1 ]
if ffunc == "chebyshev" :
output = _find_cont_fitfunc ( fluxes [ : , start : stop ] , ivars [ : , start : stop ] , contmask [ start : stop ] ... |
def _generate_random_node_values ( height ) :
"""Return random node values for building binary trees .
: param height : Height of the binary tree .
: type height : int
: return : Randomly generated node values .
: rtype : [ int ]""" | max_node_count = 2 ** ( height + 1 ) - 1
node_values = list ( range ( max_node_count ) )
random . shuffle ( node_values )
return node_values |
def usermacro_update ( hostmacroid , value , ** kwargs ) :
'''Update existing host usermacro .
: param hostmacroid : id of the host usermacro
: param value : new value of the host usermacro
: param _ connection _ user : Optional - zabbix user ( can also be set in opts or pillar , see module ' s docstring )
... | conn_args = _login ( ** kwargs )
ret = { }
try :
if conn_args :
params = { }
method = 'usermacro.update'
params [ 'hostmacroid' ] = hostmacroid
params [ 'value' ] = value
params = _params_extend ( params , _ignore_name = True , ** kwargs )
ret = _query ( method , para... |
def Authenticate ( self , app_id , challenge , registered_keys ) :
"""Authenticates app _ id with the security key .
Executes the U2F authentication / signature flow with the security key .
Args :
app _ id : The app _ id to register the security key against .
challenge : Server challenge passed to the secur... | client_data = model . ClientData ( model . ClientData . TYP_AUTHENTICATION , challenge , self . origin )
app_param = self . InternalSHA256 ( app_id )
challenge_param = self . InternalSHA256 ( client_data . GetJson ( ) )
num_invalid_keys = 0
for key in registered_keys :
try :
if key . version != u'U2F_V2' :
... |
def overloaded_build ( type_ , add_name = None ) :
"""Factory for constant transformers that apply to a given
build instruction .
Parameters
type _ : type
The object type to overload the construction of . This must be one of
" buildable " types , or types with a " BUILD _ * " instruction .
add _ name : ... | typename = type_ . __name__
instrname = 'BUILD_' + typename . upper ( )
dict_ = OrderedDict ( __doc__ = dedent ( """
A CodeTransformer for overloading {name} instructions.
""" . format ( name = instrname ) ) )
try :
build_instr = getattr ( instructions , instrname )
except AttributeError :
... |
def roll_data ( self , data ) :
"""Append new data to the right side of every line strip and remove
as much data from the left .
Parameters
data : array - like
A data array to append .""" | data = data . astype ( 'float32' ) [ ... , np . newaxis ]
s1 = self . _data_shape [ 1 ] - self . _offset
if data . shape [ 1 ] > s1 :
self . _pos_tex [ : , self . _offset : ] = data [ : , : s1 ]
self . _pos_tex [ : , : data . shape [ 1 ] - s1 ] = data [ : , s1 : ]
self . _offset = ( self . _offset + data . ... |
def get_assessments_taken ( self ) :
"""Gets all ` ` AssessmentTaken ` ` elements .
In plenary mode , the returned list contains all known
assessments taken or an error results . Otherwise , the returned
list may contain only those assessments taken that are
accessible through this session .
return : ( os... | # Implemented from template for
# osid . resource . ResourceLookupSession . get _ resources
# NOTE : This implementation currently ignores plenary view
collection = JSONClientValidated ( 'assessment' , collection = 'AssessmentTaken' , runtime = self . _runtime )
result = collection . find ( self . _view_filter ( ) ) . ... |
def warn_deprecated ( message , stacklevel = 2 ) : # pragma : no cover
"""Warn deprecated .""" | warnings . warn ( message , category = DeprecationWarning , stacklevel = stacklevel ) |
def iter_ROOT_classes ( ) :
"""Iterator over all available ROOT classes""" | class_index = "http://root.cern.ch/root/html/ClassIndex.html"
for s in minidom . parse ( urlopen ( class_index ) ) . getElementsByTagName ( "span" ) :
if ( "class" , "typename" ) in s . attributes . items ( ) :
class_name = s . childNodes [ 0 ] . nodeValue
try :
yield getattr ( QROOT , c... |
def predict_retinotopy ( sub , template = 'benson14' , registration = 'fsaverage' ) :
'''predict _ retinotopy ( subject ) yields a pair of dictionaries each with four keys : angle , eccen ,
sigma , and varea . Each of these keys maps to a numpy array with one entry per vertex . The
first element of the yielded ... | template = template . lower ( )
retino_tmpls = predict_retinotopy . retinotopy_templates [ registration ]
hemis = [ 'lh' , 'rh' ] if registration == 'fsaverage' else [ 'sym' ]
if template not in retino_tmpls :
libdir = os . path . join ( library_path ( ) , 'data' )
search_paths = [ libdir ]
# just hard - ba... |
def line ( self , plunge , bearing , * args , ** kwargs ) :
"""Plot points representing linear features on the axes . Additional
arguments and keyword arguments are passed on to ` plot ` .
Parameters
plunge , bearing : number or sequence of numbers
The plunge and bearing of the line ( s ) in degrees . The p... | lon , lat = stereonet_math . line ( plunge , bearing )
args , kwargs = self . _point_plot_defaults ( args , kwargs )
return self . plot ( [ lon ] , [ lat ] , * args , ** kwargs ) |
def read_xml ( self ) :
"""read metadata from xml and set all the found properties .
: return : the root element of the xml
: rtype : ElementTree . Element""" | if self . xml_uri is None :
root = self . _read_xml_db ( )
else :
root = self . _read_xml_file ( )
if root is not None :
for name , path in list ( self . _standard_properties . items ( ) ) :
value = read_property_from_xml ( root , path )
if value is not None : # this calls the default setter... |
def _remove_subsequent_result_because_of_batch_failure ( self , sig ) :
"""Remove transactions from scheduled and txn _ results for
successors of txns in a failed batch . These transactions will now ,
or in the future be rescheduled in next _ transaction ; giving a
replay ability .
Args :
sig ( str ) : Tr... | batch = self . _batches_by_txn_id [ sig ]
seen = [ ]
for txn in batch . transactions :
txn_id = txn . header_signature
for poss_successor in self . _scheduled . copy ( ) :
if not self . is_transaction_in_schedule ( poss_successor ) :
continue
if self . _is_txn_to_replay ( txn_id , po... |
def confirmation_option ( * param_decls , ** attrs ) :
"""Shortcut for confirmation prompts that can be ignored by passing
` ` - - yes ` ` as parameter .
This is equivalent to decorating a function with : func : ` option ` with
the following parameters : :
def callback ( ctx , param , value ) :
if not val... | def decorator ( f ) :
def callback ( ctx , param , value ) :
if not value :
ctx . abort ( )
attrs . setdefault ( 'is_flag' , True )
attrs . setdefault ( 'callback' , callback )
attrs . setdefault ( 'expose_value' , False )
attrs . setdefault ( 'prompt' , 'Do you want to continue?... |
def osmlem ( op , x , data , niter , callback = None , ** kwargs ) :
r"""Ordered Subsets Maximum Likelihood Expectation Maximation algorithm .
This solver attempts to solve : :
max _ x L ( x | data )
where ` ` L ( x , | data ) ` ` is the likelihood of ` ` x ` ` given ` ` data ` ` . The
likelihood depends on... | n_ops = len ( op )
if len ( data ) != n_ops :
raise ValueError ( 'number of data ({}) does not match number of ' 'operators ({})' . format ( len ( data ) , n_ops ) )
if not all ( x in opi . domain for opi in op ) :
raise ValueError ( '`x` not an element in the domains of all operators' )
# Convert data to range... |
def encode_quorum ( self , rw ) :
"""Converts a symbolic quorum value into its on - the - wire
equivalent .
: param rw : the quorum
: type rw : string , integer
: rtype : integer""" | if rw in QUORUM_TO_PB :
return QUORUM_TO_PB [ rw ]
elif type ( rw ) is int and rw >= 0 :
return rw
else :
return None |
def mxnet_prefer_gpu ( ) :
"""If gpu available return gpu , else cpu
Returns
context : Context
The preferable GPU context .""" | gpu = int ( os . environ . get ( 'MXNET_GPU' , default = 0 ) )
if gpu in mx . test_utils . list_gpus ( ) :
return mx . gpu ( gpu )
return mx . cpu ( ) |
def get ( key , service = None , profile = None ) : # pylint : disable = W0613
'''Get a value from the etcd service''' | client = _get_conn ( profile )
result = client . get ( key )
return result . value |
def apply_getters ( self , task ) :
"""This function is called when we specify the task dependencies with the syntax :
deps = { node : " @ property " }
In this case the task has to the get ` property ` from ` node ` before starting the calculation .
At present , the following properties are supported :
- @ ... | if not self . getters :
return
for getter in self . getters :
if getter == "@structure" :
task . history . info ( "Getting structure from %s" % self . node )
new_structure = self . node . get_final_structure ( )
task . _change_structure ( new_structure )
else :
raise ValueErr... |
def guess_strategy_type ( file_name_or_ext ) :
"""Guess strategy type to use for file by extension .
Args :
file _ name _ or _ ext : Either a file name with an extension or just
an extension
Returns :
Strategy : Type corresponding to extension or None if there ' s no
corresponding strategy type""" | if '.' not in file_name_or_ext :
ext = file_name_or_ext
else :
name , ext = os . path . splitext ( file_name_or_ext )
ext = ext . lstrip ( '.' )
file_type_map = get_file_type_map ( )
return file_type_map . get ( ext , None ) |
def get_minor_version ( version , remove = None ) :
"""Return minor version of a provided version string . Minor version is the
second component in the dot - separated version string . For non - version - like
strings this function returns ` ` None ` ` .
The ` ` remove ` ` parameter is deprecated since versio... | if remove :
warnings . warn ( "remove argument is deprecated" , DeprecationWarning )
version_split = version . split ( "." )
try : # Assume MAJOR . MINOR . REST . . .
return version_split [ 1 ]
except IndexError :
return None |
def expect ( self , use_proportions = True ) :
"""The Expectation step of the CEM algorithm""" | changed = self . get_changed ( self . partition , self . prev_partition )
lk_table = self . generate_lktable ( self . partition , changed , use_proportions )
self . table = self . likelihood_table_to_probs ( lk_table ) |
def build_kernel ( self ) :
"""Build the KNN kernel .
Build a k nearest neighbors kernel , optionally with alpha decay .
If ` precomputed ` is not ` None ` , the appropriate steps in the kernel
building process are skipped .
Must return a symmetric matrix
Returns
K : kernel matrix , shape = [ n _ sample... | if self . precomputed == "affinity" : # already done
# TODO : should we check that precomputed matrices look okay ?
# e . g . check the diagonal
K = self . data_nu
elif self . precomputed == "adjacency" : # need to set diagonal to one to make it an affinity matrix
K = self . data_nu
if sparse . issparse ( K... |
def moves_from_games ( self , start_game , end_game , moves , shuffle , column_family , column ) :
"""Dataset of samples and / or shuffled moves from game range .
Args :
n : an integer indicating how many past games should be sourced .
moves : an integer indicating how many moves should be sampled
from thos... | start_row = ROW_PREFIX . format ( start_game )
end_row = ROW_PREFIX . format ( end_game )
# NOTE : Choose a probability high enough to guarantee at least the
# required number of moves , by using a slightly lower estimate
# of the total moves , then trimming the result .
total_moves = self . count_moves_in_game_range (... |
def _filter_matrix_rows ( cls , matrix ) :
'''matrix = output from _ to _ matrix''' | indexes_to_keep = [ ]
for i in range ( len ( matrix ) ) :
keep_row = False
for element in matrix [ i ] :
if element not in { 'NA' , 'no' } :
keep_row = True
break
if keep_row :
indexes_to_keep . append ( i )
return [ matrix [ i ] for i in indexes_to_keep ] |
def _sanity_check_mark_location_preceding_optional_traverse ( ir_blocks ) :
"""Assert that optional Traverse blocks are preceded by a MarkLocation .""" | # Once all fold blocks are removed , each optional Traverse must have
# a MarkLocation block immediately before it .
_ , new_ir_blocks = extract_folds_from_ir_blocks ( ir_blocks )
for first_block , second_block in pairwise ( new_ir_blocks ) : # Traverse blocks with optional = True are immediately preceded by a MarkLoca... |
def _generate_default_grp_constraints ( roles , network_constraints ) :
"""Generate default symetric grp constraints .""" | default_delay = network_constraints . get ( 'default_delay' )
default_rate = network_constraints . get ( 'default_rate' )
default_loss = network_constraints . get ( 'default_loss' , 0 )
except_groups = network_constraints . get ( 'except' , [ ] )
grps = network_constraints . get ( 'groups' , roles . keys ( ) )
# expand... |
def sample ( self , nsamples , nburn = 0 , nthin = 1 , save_hidden_state_trajectory = False , call_back = None ) :
"""Sample from the BHMM posterior .
Parameters
nsamples : int
The number of samples to generate .
nburn : int , optional , default = 0
The number of samples to discard to burn - in , followin... | # Run burn - in .
for iteration in range ( nburn ) :
logger ( ) . info ( "Burn-in %8d / %8d" % ( iteration , nburn ) )
self . _update ( )
# Collect data .
models = list ( )
for iteration in range ( nsamples ) :
logger ( ) . info ( "Iteration %8d / %8d" % ( iteration , nsamples ) )
# Run a number of Gi... |
def invariant_image_similarity ( image1 , image2 , local_search_iterations = 0 , metric = 'MI' , thetas = np . linspace ( 0 , 360 , 5 ) , thetas2 = np . linspace ( 0 , 360 , 5 ) , thetas3 = np . linspace ( 0 , 360 , 5 ) , scale_image = 1 , do_reflection = False , txfn = None , transform = 'Affine' ) :
"""Similarity... | if transform not in { 'Rigid' , 'Similarity' , 'Affine' } :
raise ValueError ( 'transform must be one of Rigid/Similarity/Affine' )
if image1 . pixeltype != 'float' :
image1 = image1 . clone ( 'float' )
if image2 . pixeltype != 'float' :
image2 = image2 . clone ( 'float' )
if txfn is None :
txfn = mktem... |
def fix_pbc ( structure , matrix = None ) :
"""Set all frac _ coords of the input structure within [ 0,1 ] .
Args :
structure ( pymatgen structure object ) :
input structure
matrix ( lattice matrix , 3 by 3 array / matrix )
new structure ' s lattice matrix , if none , use
input structure ' s matrix
Re... | spec = [ ]
coords = [ ]
if matrix is None :
latte = Lattice ( structure . lattice . matrix )
else :
latte = Lattice ( matrix )
for site in structure :
spec . append ( site . specie )
coord = np . array ( site . frac_coords )
for i in range ( 3 ) :
coord [ i ] -= floor ( coord [ i ] )
... |
def unpack_response ( self , cursor_id = None , codec_options = _UNICODE_REPLACE_CODEC_OPTIONS , user_fields = None , legacy_response = False ) :
"""Unpack a OP _ MSG command response .
: Parameters :
- ` cursor _ id ` ( optional ) : Ignored , for compatibility with _ OpReply .
- ` codec _ options ` ( optiona... | # If _ OpMsg is in - use , this cannot be a legacy response .
assert not legacy_response
return bson . _decode_all_selective ( self . payload_document , codec_options , user_fields ) |
def load_tags ( self , max_pages = 30 ) :
"""Load all WordPress tags from the given site .
: param max _ pages : kill counter to avoid infinite looping
: return : None""" | logger . info ( "loading tags" )
# clear them all out so we don ' t get dupes if requested
if self . purge_first :
Tag . objects . filter ( site_id = self . site_id ) . delete ( )
path = "sites/{}/tags" . format ( self . site_id )
params = { "number" : 1000 }
page = 1
response = self . get ( path , params )
if not ... |
def browse_history ( self , backward ) :
"""Browse history""" | if self . is_cursor_before ( 'eol' ) and self . hist_wholeline :
self . hist_wholeline = False
tocursor = self . get_current_line_to_cursor ( )
text , self . histidx = self . find_in_history ( tocursor , self . histidx , backward )
if text is not None :
if self . hist_wholeline :
self . clear_line ( )
... |
def butter ( dt_list , val , lowpass = 1.0 ) :
"""This is framework for a butterworth bandpass for 1D data
Needs to be cleaned up and generalized""" | import scipy . signal
import matplotlib . pyplot as plt
# dt is 300 s , 5 min
dt_diff = np . diff ( dt_list )
dt_diff = np . array ( [ dt . total_seconds ( ) for dt in dt_diff ] )
dt = malib . fast_median ( dt_diff )
# f is 0.00333 Hz
# 288 samples / day
fs = 1. / dt
nyq = fs / 2.
if False : # psd , f = psd ( z _ msl ,... |
def item_path_or ( default , keys , dict_or_obj ) :
"""Optional version of item _ path with a default value . keys can be dict keys or object attributes , or a combination
: param default :
: param keys : List of keys or dot - separated string
: param dict _ or _ obj : A dict or obj
: return :""" | if not keys :
raise ValueError ( "Expected at least one key, got {0}" . format ( keys ) )
resolved_keys = keys . split ( '.' ) if isinstance ( str , keys ) else keys
current_value = dict_or_obj
for key in resolved_keys :
current_value = prop_or ( default , key , default_to ( { } , current_value ) )
return curre... |
async def power ( dev : Device , cmd , target , value ) :
"""Turn on and off , control power settings .
Accepts commands ' on ' , ' off ' , and ' settings ' .""" | async def try_turn ( cmd ) :
state = True if cmd == "on" else False
try :
return await dev . set_power ( state )
except SongpalException as ex :
if ex . code == 3 :
err ( "The device is already %s." % cmd )
else :
raise ex
if cmd == "on" or cmd == "off" :
... |
def cmd_gyrocal ( self , args ) :
'''do a full gyro calibration''' | mav = self . master
mav . mav . command_long_send ( mav . target_system , mav . target_component , mavutil . mavlink . MAV_CMD_PREFLIGHT_CALIBRATION , 0 , 1 , 0 , 0 , 0 , 0 , 0 , 0 ) |
def _makeplot ( self , ax , fig , data , ymin = None , ymax = None , height = 6 , width = 6 , dos = None , color = None ) :
"""Utility method to tidy phonon band structure diagrams .""" | # Define colours
if color is None :
color = 'C0'
# Default to first colour in matplotlib series
# set x and y limits
tymax = ymax if ( ymax is not None ) else max ( flatten ( data [ 'frequency' ] ) )
tymin = ymin if ( ymin is not None ) else min ( flatten ( data [ 'frequency' ] ) )
pad = ( tymax - tymin ) * 0.05
if... |
def build_D3treepie ( old , MAX_DEPTH , level = 1 , toplayer = None ) :
"""Create the JSON needed by the treePie viz
http : / / bl . ocks . org / adewes / 4710330/94a7c0aeb6f09d681dbfdd0e5150578e4935c6ae
Eg
[ ' origin ' , [ n1 , n2 ] ,
{ ' name1 ' :
[ ' name1 ' , [ n1 , n2 ] ,
{ ' name1-1 ' : . . . }""" | d = { }
if not old :
old = toplayer
for x in old :
label = x . bestLabel ( quotes = False ) . replace ( "_" , " " )
if x . children ( ) and level < MAX_DEPTH :
size = len ( x . children ( ) )
d [ x . qname ] = [ label , [ size , size ] , build_D3treepie ( x . children ( ) , MAX_DEPTH , level... |
def get_eval_func ( obj , feature , slice = np . s_ [ ... ] ) :
"""Return the function of interest ( kernel or mean ) for the expectation
depending on the type of : obj : and whether any features are given""" | if feature is not None : # kernel + feature combination
if not isinstance ( feature , InducingFeature ) or not isinstance ( obj , kernels . Kernel ) :
raise TypeError ( "If `feature` is supplied, `obj` must be a kernel." )
return lambda x : tf . transpose ( Kuf ( feature , obj , x ) ) [ slice ]
elif isi... |
def _to_power_basis_degree4 ( nodes1 , nodes2 ) :
r"""Compute the coefficients of an * * intersection polynomial * * .
Helper for : func : ` to _ power _ basis ` in the case that B | eacute | zout ' s
` theorem ` _ tells us the * * intersection polynomial * * is degree
: math : ` 4 ` . This happens if the two... | # We manually invert the Vandermonde matrix :
# [1 0 0 0 0 ] [ c0 ] = [ n0]
# [1 1/4 1/16 1/64 1/256 ] [ c1 ] [ n1]
# [1 1/2 1/4 1/8 1/16 ] [ c2 ] [ n2]
# [1 3/4 9/16 27/64 81/256 ] [ c3 ] [ n3]
# [1 1 1 1 1 ] [ c4 ] [ n4]
val0 = eval_intersection_polynomial ( nodes1 , nodes2 , 0.0 )
val1 = eval_intersection_polynomial... |
def score_for_percentile_in ( self , leaderboard_name , percentile ) :
'''Calculate the score for a given percentile value in the leaderboard .
@ param leaderboard _ name [ String ] Name of the leaderboard .
@ param percentile [ float ] Percentile value ( 0.0 to 100.0 inclusive ) .
@ return the score correspo... | if not 0 <= percentile <= 100 :
return None
total_members = self . total_members_in ( leaderboard_name )
if total_members < 1 :
return None
if self . order == self . ASC :
percentile = 100 - percentile
index = ( total_members - 1 ) * ( percentile / 100.0 )
scores = [ pair [ 1 ] for pair in self . redis_conn... |
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