signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def importSNPs ( packageFile ) :
"""The big wrapper , this function should detect the SNP type by the package manifest and then launch the corresponding function .
Here ' s an example of a SNP manifest file for Casava SNPs : :
[ package _ infos ]
description = Casava SNPs for testing purposes
maintainer = T... | printf ( "Importing polymorphism set: %s... (This may take a while)" % packageFile )
isDir = False
if not os . path . isdir ( packageFile ) :
packageDir = _decompressPackage ( packageFile )
else :
isDir = True
packageDir = packageFile
fpMan = os . path . normpath ( packageDir + '/manifest.ini' )
if not os .... |
def access_token_response ( self , token , message_id = None ) :
"""Access token response structure .
Success if token is set , otherwise ( None , empty string ) give error
response . If message _ id is set then an extra messageId attribute is
set in the response to handle postMessage ( ) responses .""" | if ( token ) :
data = { "accessToken" : token , "expiresIn" : self . access_token_lifetime }
if ( message_id ) :
data [ 'messageId' ] = message_id
else :
data = { "error" : "client_unauthorized" , "description" : "No authorization details received" }
return data |
def run ( self ) :
'''Start a Master Worker''' | salt . utils . process . appendproctitle ( self . name )
self . clear_funcs = ClearFuncs ( self . opts , self . key , )
self . aes_funcs = AESFuncs ( self . opts )
salt . utils . crypt . reinit_crypto ( )
self . __bind ( ) |
def human_duration ( duration_seconds : float ) -> str :
"""Convert a duration in seconds into a human friendly string .""" | if duration_seconds < 0.001 :
return '0 ms'
if duration_seconds < 1 :
return '{} ms' . format ( int ( duration_seconds * 1000 ) )
return '{} s' . format ( int ( duration_seconds ) ) |
def setup_logging ( self ) :
"""Configure the logging framework .""" | if self . config . debug :
util . setup_logging ( level = logging . DEBUG )
util . activate_debug_shell_on_signal ( )
else :
util . setup_logging ( level = logging . INFO ) |
def read_proxy ( fl ) :
"""Read a file to create a proxy record instance""" | outcore = ProxyRecord ( data = pd . read_csv ( fl , sep = r'\s*\,\s*' , index_col = None , engine = 'python' ) )
return outcore |
def clean ( self ) :
'''Either staffCategory or staffMember must be filled in , but not both .''' | if not self . staffCategory and not self . staffMember :
raise ValidationError ( _ ( 'Either staff category or staff member must be specified.' ) )
if self . staffCategory and self . staffMember :
raise ValidationError ( _ ( 'Specify either a staff category or a staff member, not both.' ) ) |
def _run_events ( self , tag , stage = None ) :
"""Run tests marked with a particular tag and stage""" | self . _run_event_methods ( tag , stage )
self . _run_tests ( tag , stage ) |
def update_fitness ( objective_function , particle ) :
"""Calculates and updates the fitness and best _ fitness of a particle .
Fitness is calculated using the ' problem . fitness ' function .
Args :
problem : The optimization problem encapsulating the fitness function
and optimization type .
particle : c... | fitness = objective_function ( particle . position )
best_fitness = particle . best_fitness
cmp = comparator ( fitness )
if best_fitness is None or cmp ( fitness , best_fitness ) :
best_position = particle . position
return particle . _replace ( fitness = fitness , best_fitness = fitness , best_position = best_... |
def lsb_release ( self , loglevel = logging . DEBUG ) :
"""Get distro information from lsb _ release .""" | # v the space is intentional , to avoid polluting bash history .
shutit = self . shutit
d = { }
self . send ( ShutItSendSpec ( self , send = ' command lsb_release -a' , check_exit = False , echo = False , loglevel = loglevel , ignore_background = True ) )
res = shutit . match_string ( self . pexpect_child . before , r'... |
def inverse_kinematic_optimization ( chain , target_frame , starting_nodes_angles , regularization_parameter = None , max_iter = None ) :
"""Computes the inverse kinematic on the specified target with an optimization method
Parameters
chain : ikpy . chain . Chain
The chain used for the Inverse kinematics .
... | # Only get the position
target = target_frame [ : 3 , 3 ]
if starting_nodes_angles is None :
raise ValueError ( "starting_nodes_angles must be specified" )
# Compute squared distance to target
def optimize_target ( x ) : # y = np . append ( starting _ nodes _ angles [ : chain . first _ active _ joint ] , x )
y ... |
def translate ( obj , vec , ** kwargs ) :
"""Translates curves , surface or volumes by the input vector .
Keyword Arguments :
* ` ` inplace ` ` : if False , operation applied to a copy of the object . * Default : False *
: param obj : input geometry
: type obj : abstract . SplineGeometry or multi . Abstract... | # Input validity checks
if not vec or not isinstance ( vec , ( tuple , list ) ) :
raise GeomdlException ( "The input must be a list or a tuple" )
# Input validity checks
if len ( vec ) != obj . dimension :
raise GeomdlException ( "The input vector must have " + str ( obj . dimension ) + " components" )
# Keywor... |
def save ( self , name , data , location = 'local' , kind = 'json' ) :
"""Save a dictionary in a JSON file within the cache directory .""" | file_ext = '.json' if kind == 'json' else '.pkl'
path = self . _get_path ( name , location , file_ext = file_ext )
_ensure_dir_exists ( op . dirname ( path ) )
logger . debug ( "Save data to `%s`." , path )
if kind == 'json' :
_save_json ( path , data )
else :
_save_pickle ( path , data ) |
def format_key_from_backend ( self , key ) :
"""Strip the configured prefix from a key retrieved from the backend
before passing it on to other pghoard code and presenting it to the
user .""" | if not self . prefix :
return key
if not key . startswith ( self . prefix ) :
raise StorageError ( "Key {!r} does not start with expected prefix {!r}" . format ( key , self . prefix ) )
return key [ len ( self . prefix ) : ] |
def decode_json ( cls , dct ) :
'''Custom JSON decoder for Events .
Can be used as the ` ` object _ hook ` ` argument of ` ` json . load ` ` or
` ` json . loads ` ` .
Args :
dct ( dict ) : a JSON dictionary to decode
The dictionary should have keys ` ` event _ name ` ` and ` ` event _ values ` `
Raises ... | if not ( 'event_name' in dct and 'event_values' in dct ) :
return dct
event_name = dct [ 'event_name' ]
if event_name not in _CONCRETE_EVENT_CLASSES :
raise ValueError ( "Could not find appropriate Event class for event_name: %r" % event_name )
event_values = dct [ 'event_values' ]
model_id = event_values . pop... |
def _send_to_destination ( self , destination , header , payload , transport_kwargs , add_path_step = True ) :
"""Helper function to send a message to a specific recipe destination .""" | if header :
header = header . copy ( )
header [ "workflows-recipe" ] = True
else :
header = { "workflows-recipe" : True }
dest_kwargs = transport_kwargs . copy ( )
if ( "transport-delay" in self . recipe [ destination ] and "delay" not in transport_kwargs ) :
dest_kwargs [ "delay" ] = self . recipe [ de... |
async def packages ( self , package_state : Union [ int , str ] = '' , show_archived : bool = False ) -> list :
"""Get the list of packages associated with the account .""" | packages_resp = await self . _request ( 'post' , API_URL_BUYER , json = { 'version' : '1.0' , 'method' : 'GetTrackInfoList' , 'param' : { 'IsArchived' : show_archived , 'Item' : '' , 'Page' : 1 , 'PerPage' : 40 , 'PackageState' : package_state , 'Sequence' : '0' } , 'sourcetype' : 0 } )
_LOGGER . debug ( 'Packages resp... |
def list_milestones ( page_size = 200 , page_index = 0 , q = "" , sort = "" ) :
"""List all ProductMilestones""" | data = list_milestones_raw ( page_size , page_index , sort , q )
if data :
return utils . format_json_list ( data ) |
def backward_committor_sensitivity ( T , A , B , index ) :
"""calculate the sensitivity matrix for index of the backward committor from A to B given transition matrix T .
Parameters
T : numpy . ndarray shape = ( n , n )
Transition matrix
A : array like
List of integer state labels for set A
B : array li... | # This is really ugly to compute . The problem is , that changes in T induce changes in
# the stationary distribution and so we need to add this influence , too
# I implemented something which is correct , but don ' t ask me about the derivation
n = len ( T )
trT = numpy . transpose ( T )
one = numpy . ones ( n )
eq = ... |
def _idle_loop ( self ) :
"""This is used to exec the idle function in a safe context and a separate thread""" | while not self . _stop_update_flag :
time . sleep ( self . update_interval )
with self . update_lock :
try :
self . idle ( )
except :
self . _log . error ( "exception in App.idle method" , exc_info = True )
if self . _need_update_flag :
try :
... |
def read_dirs ( path , folder ) :
'''Fetches name of all files in path in long form , and labels associated by extrapolation of directory names .''' | lbls , fnames , all_lbls = [ ] , [ ] , [ ]
full_path = os . path . join ( path , folder )
for lbl in sorted ( os . listdir ( full_path ) ) :
if lbl not in ( '.ipynb_checkpoints' , '.DS_Store' ) :
all_lbls . append ( lbl )
for fname in os . listdir ( os . path . join ( full_path , lbl ) ) :
... |
def greenhall_sw ( t , alpha ) :
"""Eqn ( 7 ) from Greenhall2004""" | alpha = int ( alpha )
if alpha == 2 :
return - np . abs ( t )
elif alpha == 1 :
if t == 0 :
return 0
else :
return pow ( t , 2 ) * np . log ( np . abs ( t ) )
elif alpha == 0 :
return np . abs ( pow ( t , 3 ) )
elif alpha == - 1 :
if t == 0 :
return 0
else :
retur... |
def blacklist ( db , term = None ) :
"""List the blacklisted entities available in the registry .
The function will return the list of blacklisted entities . If term
parameter is set , it will only return the information about the
entities which match that term . When the given term does not match
with any ... | mbs = [ ]
with db . connect ( ) as session :
if term :
mbs = session . query ( MatchingBlacklist ) . filter ( MatchingBlacklist . excluded . like ( '%' + term + '%' ) ) . order_by ( MatchingBlacklist . excluded ) . all ( )
if not mbs :
raise NotFoundError ( entity = term )
else :
... |
def _to_scientific_tuple ( number ) :
r"""Return mantissa and exponent of a number expressed in scientific notation .
Full precision is maintained if the number is represented as a string .
: param number : Number
: type number : integer , float or string
: rtype : Tuple whose first item is the mantissa ( *... | # pylint : disable = W0632
if isinstance ( number , bool ) or ( not isinstance ( number , ( int , float , str ) ) ) :
raise RuntimeError ( "Argument `number` is not valid" )
convert = not isinstance ( number , str )
# Detect zero and return , simplifies subsequent algorithm
if ( convert and ( not number ) ) or ( ( ... |
def find_min_required ( path ) :
"""Inspect terraform files and find minimum version .""" | found_min_required = ''
for filename in glob . glob ( os . path . join ( path , '*.tf' ) ) :
with open ( filename , 'r' ) as stream :
tf_config = hcl . load ( stream )
if tf_config . get ( 'terraform' , { } ) . get ( 'required_version' ) :
found_min_required = tf_config . get ( 'terrafor... |
def upgrade ( reboot = False , at_time = None ) :
'''Upgrade the kernel and optionally reboot the system .
reboot : False
Request a reboot if a new kernel is available .
at _ time : immediate
Schedule the reboot at some point in the future . This argument
is ignored if ` ` reboot = False ` ` . See
: py ... | result = __salt__ [ 'pkg.upgrade' ] ( name = _package_name ( ) )
_needs_reboot = needs_reboot ( )
ret = { 'upgrades' : result , 'active' : active ( ) , 'latest_installed' : latest_installed ( ) , 'reboot_requested' : reboot , 'reboot_required' : _needs_reboot }
if reboot and _needs_reboot :
log . warning ( 'Rebooti... |
def from_geom ( geom ) :
"""Create and return a position object for the geom
Parameters
geom : geom
An instantiated geom object .
Returns
out : position
A position object
Raises : class : ` PlotnineError ` if unable to create a ` position ` .""" | name = geom . params [ 'position' ]
if issubclass ( type ( name ) , position ) :
return name
if isinstance ( name , type ) and issubclass ( name , position ) :
klass = name
elif is_string ( name ) :
if not name . startswith ( 'position_' ) :
name = 'position_{}' . format ( name )
klass = Registr... |
def set_unspents ( self , unspents ) :
"""Set the unspent inputs for a transaction .
: param unspents : a list of : class : ` TxOut ` ( or the subclass : class : ` Spendable ` ) objects
corresponding to the : class : ` TxIn ` objects for this transaction ( same number of
items in each list )""" | if len ( unspents ) != len ( self . txs_in ) :
raise ValueError ( "wrong number of unspents" )
self . unspents = unspents |
def compute_l_from_MCMC ( self , X , n = 0 , sampler = None , flat_trace = None , burn = 0 , thin = 1 , ** kwargs ) :
"""Compute desired quantities from MCMC samples of the hyperparameter posterior .
The return will be a list with a number of rows equal to the number of
hyperparameter samples . The columns will... | if flat_trace is None :
if sampler is None :
sampler = self . sample_hyperparameter_posterior ( burn = burn , ** kwargs )
# If we create the sampler , we need to make sure we clean up
# its pool :
try :
sampler . pool . close ( )
except AttributeError : # This wil... |
def register_binary_type ( content_type , dumper , loader ) :
"""Register handling for a binary content type .
: param str content _ type : content type to register the hooks for
: param dumper : called to decode bytes into a dictionary .
Calling convention : ` ` dumper ( obj _ dict ) - > bytes ` ` .
: para... | content_type = headers . parse_content_type ( content_type )
content_type . parameters . clear ( )
key = str ( content_type )
_content_types [ key ] = content_type
handler = _content_handlers . setdefault ( key , _ContentHandler ( key ) )
handler . dict_to_bytes = dumper
handler . bytes_to_dict = loader |
def opensignals_hierarchy ( root = None , update = False , clone = False ) :
"""Brief
Function that generates the OpenSignalsTools Notebooks File Hierarchy programatically .
Description
OpenSignalsTools Notebooks folder obey to a predefined hierarchy that allows to run the code of online available
notebooks... | if root is None :
root = os . getcwd ( )
categories = list ( NOTEBOOK_KEYS . keys ( ) )
# = = = = = Creation of the main directory = = = = =
current_dir = root + "/biosignalsnotebooks_environment"
if not os . path . isdir ( current_dir ) :
os . makedirs ( current_dir )
# = = = = = Copy of ' images ' ' styles ' ... |
def make_directory_writable ( dirname ) :
"""Makes directory readable and writable by everybody .
Args :
dirname : name of the directory
Returns :
True if operation was successfull
If you run something inside Docker container and it writes files , then
these files will be written as root user with restr... | retval = shell_call ( [ 'docker' , 'run' , '-v' , '{0}:/output_dir' . format ( dirname ) , 'busybox:1.27.2' , 'chmod' , '-R' , 'a+rwx' , '/output_dir' ] )
if not retval :
logging . error ( 'Failed to change permissions on directory: %s' , dirname )
return retval |
def servers_with_roles ( self , roles , env = None , match_all = False ) :
"""Get servers with the given roles . If env is given , then the environment must match as well .
If match _ all is True , then only return servers who have all of the given roles . Otherwise ,
return servers that have one or more of the... | result = [ ]
roles = set ( roles )
for instance in self . server_details ( ) :
instroles = set ( instance [ 'roles' ] )
envmatches = ( env is None ) or ( instance [ 'environment' ] == env )
if envmatches and match_all and roles <= instroles :
result . append ( instance )
elif envmatches and not ... |
def dtraj_T100K_dt10_n ( self , divides ) :
"""100K frames trajectory at timestep 10 , arbitrary n - state discretization .""" | disc = np . zeros ( 100 , dtype = int )
divides = np . concatenate ( [ divides , [ 100 ] ] )
for i in range ( len ( divides ) - 1 ) :
disc [ divides [ i ] : divides [ i + 1 ] ] = i + 1
return disc [ self . dtraj_T100K_dt10 ] |
def ecef2geodetic_old ( x : float , y : float , z : float , ell : Ellipsoid = None , deg : bool = True ) -> Tuple [ float , float , float ] :
"""convert ECEF ( meters ) to geodetic coordinates
input
x , y , z [ meters ] target ECEF location [ 0 , Infinity )
ell reference ellipsoid
deg degrees input / output... | if ell is None :
ell = Ellipsoid ( )
ea = ell . a
eb = ell . b
rad = hypot ( x , y )
# Constant required for Latitude equation
rho = arctan2 ( eb * z , ea * rad )
# Constant required for latitude equation
c = ( ea ** 2 - eb ** 2 ) / hypot ( ea * rad , eb * z )
# Starter for the Newtons Iteration Method
vnew = arcta... |
def get_repo_version ( url ) :
"""Get the current version on GitHub
` url ` looks like ' https : / / raw . githubusercontent . com / aquatix / ns - notifications / master / VERSION '""" | response = requests . get ( url )
if response . status_code == 404 :
return None
else :
return response . text . replace ( '\n' , '' ) |
def get_bucket_files ( glob_pattern , base_dir , force = False , pattern_slice = slice ( None ) ) :
"""Helper function to download files from Google Cloud Storage .
Args :
glob _ pattern ( str or list ) : Glob pattern string or series of patterns
used to search for on Google Cloud Storage . The pattern should... | if gcsfs is None :
raise RuntimeError ( "Missing 'gcsfs' dependency for GCS download." )
if not os . path . isdir ( base_dir ) : # it is the caller ' s responsibility to make this
raise OSError ( "Directory does not exist: {}" . format ( base_dir ) )
if isinstance ( glob_pattern , str ) :
glob_pattern = [ g... |
def filelist ( jottapath , JFS ) :
"""Get a set ( ) of files from a jottapath ( a folder )""" | log . debug ( "filelist %r" , jottapath )
try :
jf = JFS . getObject ( jottapath )
except JFSNotFoundError :
return set ( )
# folder does not exist , so pretend it is an empty folder
if not isinstance ( jf , JFSFolder ) :
return False
return set ( [ f . name for f in jf . files ( ) if not f . is_deleted... |
def gp_background ( ) :
"""plot background methods and S / B vs energy""" | inDir , outDir = getWorkDirs ( )
data , REBIN = OrderedDict ( ) , None
titles = [ 'SE_{+-}' , 'SE@^{corr}_{/Symbol \\261\\261}' , 'ME@^{N}_{+-}' ]
Apm = OrderedDict ( [ ( '19' , 0.026668 ) , ( '27' , 0.026554 ) , ( '39' , 0.026816 ) , ( '62' , 0.026726 ) ] )
fake = np . array ( [ [ - 1 , 1 , 0 , 0 , 0 ] ] )
lines = { '... |
def access_key_id ( ecs_access_key_id ) :
"""Display / set / update the ECS access key id .""" | if not ecs_access_key_id :
click . secho ( dtool_config . utils . get_ecs_access_key_id ( CONFIG_PATH ) )
else :
click . secho ( dtool_config . utils . set_ecs_access_key_id ( CONFIG_PATH , ecs_access_key_id ) ) |
def query ( wosclient , wos_query , xml_query = None , count = 5 , offset = 1 , limit = 100 ) :
"""Query Web of Science and XML query results with multiple requests .""" | results = [ single ( wosclient , wos_query , xml_query , min ( limit , count - x + 1 ) , x ) for x in range ( offset , count + 1 , limit ) ]
if xml_query :
return [ el for res in results for el in res ]
else :
pattern = _re . compile ( r'^<\?xml.*?\n<records>\n|\n</records>$.*' )
return ( '<?xml version="1.... |
def _handle_binary_op ( self , node , scope , ctxt , stream ) :
"""TODO : Docstring for _ handle _ binary _ op .
: node : TODO
: scope : TODO
: ctxt : TODO
: stream : TODO
: returns : TODO""" | self . _dlog ( "handling binary operation {}" . format ( node . op ) )
switch = { "+" : lambda x , y : x + y , "-" : lambda x , y : x - y , "*" : lambda x , y : x * y , "/" : lambda x , y : x / y , "|" : lambda x , y : x | y , "^" : lambda x , y : x ^ y , "&" : lambda x , y : x & y , "%" : lambda x , y : x % y , ">" : ... |
def get_ipv6_neighbors_table ( self ) :
"""Get IPv6 neighbors table information .
Return a list of dictionaries having the following set of keys :
* interface ( string )
* mac ( string )
* ip ( string )
* age ( float ) in seconds
* state ( string )
For example : :
' interface ' : ' MgmtEth0 / RSP0 /... | ipv6_neighbors_table = [ ]
command = "show ipv6 neighbors"
output = self . _send_command ( command )
ipv6_neighbors = ""
fields = re . split ( r"^IPv6\s+Address.*Interface$" , output , flags = ( re . M | re . I ) )
if len ( fields ) == 2 :
ipv6_neighbors = fields [ 1 ] . strip ( )
for entry in ipv6_neighbors . spli... |
def publish ( self , cart , env = None ) :
"""` cart ` - Release cart to publish in json format
Publish a release cart in JSON format to the pre - release environment .""" | juicer . utils . Log . log_debug ( "Initializing publish of cart '%s'" % cart . cart_name )
if not env :
env = self . _defaults [ 'start_in' ]
cart_id = juicer . utils . upload_cart ( cart , env )
juicer . utils . Log . log_debug ( '%s uploaded with an id of %s' % ( cart . cart_name , cart_id ) )
return True |
def jsonify ( self , data : Any , code : Union [ int , Tuple [ int , str , str ] ] = HTTPStatus . OK , headers : Optional [ Dict [ str , str ] ] = None , ) :
"""Convenience method to return json responses .
: param data : The python data to jsonify .
: param code : The HTTP status code to return .
: param hea... | return jsonify ( data ) , code , headers or { } |
def codemirror_settings_update ( configs , parameters , on = None , names = None ) :
"""Return a new dictionnary of configs updated with given parameters .
You may use ` ` on ` ` and ` ` names ` ` arguments to select config or filter out
some configs from returned dict .
Arguments :
configs ( dict ) : Dicti... | # Deep copy of given config
output = copy . deepcopy ( configs )
# Optionnaly filtering config from given names
if names :
output = { k : output [ k ] for k in names }
# Select every config if selectors is empty
if not on :
on = output . keys ( )
for k in on :
output [ k ] . update ( parameters )
return out... |
def makefifo ( self , tarinfo , targetpath ) :
"""Make a fifo called targetpath .""" | if hasattr ( os , "mkfifo" ) :
os . mkfifo ( targetpath )
else :
raise ExtractError ( "fifo not supported by system" ) |
def _process_phenotypicseries ( self , limit ) :
"""Creates classes from the OMIM phenotypic series list .
These are grouping classes to hook the more granular OMIM diseases .
# TEC what does ' hook ' mean here ?
: param limit :
: return :""" | if self . test_mode :
graph = self . testgraph
else :
graph = self . graph
LOG . info ( "getting phenotypic series titles" )
model = Model ( graph )
line_counter = 0
src_key = 'phenotypicSeries'
col = self . files [ src_key ] [ 'columns' ]
raw = '/' . join ( ( self . rawdir , self . files [ src_key ] [ 'file' ]... |
def new_block ( self ) :
"""create a new sub block to the current block and return it .
the sub block is added to the current block .""" | child = Block ( self , py3_wrapper = self . py3_wrapper )
self . add ( child )
return child |
def parse ( text ) :
"""Parses the dependency schema from a given string
( typically a container stdout log )""" | found = re . findall ( r'(?<=BEGIN_DEPENDENCIES_SCHEMA_OUTPUT>).*(?=<END_DEPENDENCIES_SCHEMA_OUTPUT)' , text )
dependency_results = [ ]
for match in found :
data = json . loads ( match )
validate ( data )
# will throw ValidationError if invalid
dependency_results += data [ 'dependencies' ]
# we don ' t ... |
def find_last_true ( sorted_list , true_criterion ) :
"""Suppose we have a list of item [ item1 , item2 , . . . , itemN ] .
: type array : list
: param array : an iterable object that support inex
: param x : a comparable value
If we do a mapping : :
> > > def true _ criterion ( item ) :
. . . return it... | # exam first item , if not true , then impossible to find result
if not true_criterion ( sorted_list [ 0 ] ) :
raise ValueError
# exam last item , if true , it is the one .
if true_criterion ( sorted_list [ - 1 ] ) :
return sorted_list [ - 1 ]
lower , upper = 0 , len ( sorted_list ) - 1
index = int ( ( lower + ... |
def _send_event_task ( args ) :
"""Actually sends the MixPanel event . Runs in a uwsgi worker process .""" | endpoint = args [ 'endpoint' ]
json_message = args [ 'json_message' ]
_consumer_impl . send ( endpoint , json_message ) |
def _calculate_position ( self , at_line = None , at_position = None , at_point = None ) :
"""Calculate a global point position ` QPoint ( x , y ) ` , for a given
line , local cursor position , or local point .""" | # Check that no option or only one option is given :
if [ at_line , at_position , at_point ] . count ( None ) < 2 :
raise Exception ( 'Provide no argument or only one argument!' )
# Saving cursor position :
if at_position is None :
at_position = self . get_position ( 'cursor' )
# FIXME : What id this used for ?... |
def configure_error_handlers ( app ) :
"""Configure application error handlers""" | def render_error ( error ) :
return ( render_template ( 'errors/%s.html' % error . code , title = error_messages [ error . code ] , code = error . code ) , error . code )
for ( errcode , title ) in error_messages . iteritems ( ) :
app . errorhandler ( errcode ) ( render_error ) |
def k_bn ( self , n , Re ) :
"""returns normalisation of the sersic profile such that Re is the half light radius given n _ sersic slope""" | bn = self . b_n ( n )
k = bn * Re ** ( - 1. / n )
return k , bn |
def start ( self ) :
"""Start HTML output .""" | today = time . time ( )
yesterday = today - 86400
tomorrow = today + 86400
today = time . localtime ( today )
yesterday = time . localtime ( yesterday )
tomorrow = time . localtime ( tomorrow )
fn = self . fnFromDate ( today )
if os . path . exists ( fn ) :
out . warn ( 'HTML output file %r already exists' % fn )
... |
def consistency_check ( self ) :
"""Checks the network for consistency , including bus definitions and impedances .
Prints warnings if anything is potentially inconsistent .
Examples
> > > network . consistency _ check ( )""" | for c in self . iterate_components ( self . one_port_components ) :
missing = c . df . index [ ~ c . df . bus . isin ( self . buses . index ) ]
if len ( missing ) > 0 :
logger . warning ( "The following %s have buses which are not defined:\n%s" , c . list_name , missing )
for c in self . iterate_compone... |
def from_dataframe ( cls , name , df , indices , primary_key = None ) :
"""Infer table metadata from a DataFrame""" | # ordered list ( column _ name , column _ type ) pairs
column_types = [ ]
# which columns have nullable values
nullable = set ( )
# tag cached database by dataframe ' s number of rows and columns
for column_name in df . columns :
values = df [ column_name ]
if values . isnull ( ) . any ( ) :
nullable . ... |
def create_dump ( ) :
"""Create the grammar for the ' dump ' statement""" | dump = upkey ( "dump" ) . setResultsName ( "action" )
return ( dump + upkey ( "schema" ) + Optional ( Group ( delimitedList ( table ) ) . setResultsName ( "tables" ) ) ) |
def _normalize_options ( self , options ) :
"""Generator of 2 - tuples ( option - key , option - value ) .
When options spec is a list , generate a 2 - tuples per list item .
: param options : dict { option : value }
returns :
iterator ( option - key , option - value )
- option names lower cased and prepe... | for key , value in list ( options . items ( ) ) :
if '--' in key :
normalized_key = self . _normalize_arg ( key )
else :
normalized_key = '--%s' % self . _normalize_arg ( key )
if isinstance ( value , ( list , tuple ) ) :
for opt_val in value :
yield ( normalized_key , op... |
def map_run ( path = None , opts = None , ** kwargs ) :
'''Execute a salt cloud map file''' | client = _get_client ( )
if isinstance ( opts , dict ) :
client . opts . update ( opts )
info = client . map_run ( path , ** salt . utils . args . clean_kwargs ( ** kwargs ) )
return info |
def cleanUpPparse ( outputpath , rawfilename , mgf = False ) :
"""Delete temporary files generated by pparse , including the filetypes
" . csv " , " . ms1 " , " . ms2 " , " . xtract " , the files " pParsePlusLog . txt " and
" pParse . para " and optionally also the " . mgf " file generated by pParse .
. . war... | extensions = [ 'csv' , 'ms1' , 'ms2' , 'xtract' ]
filename , fileext = os . path . splitext ( os . path . basename ( rawfilename ) )
additionalFiles = [ aux . joinpath ( outputpath , 'pParsePlusLog.txt' ) , aux . joinpath ( outputpath , filename + '.pparse.para' ) , ]
for ext in extensions :
filepath = aux . joinpa... |
def add_override ( self , partname , content_type ) :
"""Add a child ` ` < Override > ` ` element with attributes set to parameter
values .""" | return self . _add_override ( partName = partname , contentType = content_type ) |
def set_cursor ( self , value ) :
"""Changes the grid cursor cell .
Parameters
value : 2 - tuple or 3 - tuple of String
\t row , col , tab or row , col for target cursor position""" | shape = self . grid . code_array . shape
if len ( value ) == 3 :
self . grid . _last_selected_cell = row , col , tab = value
if row < 0 or col < 0 or tab < 0 or row >= shape [ 0 ] or col >= shape [ 1 ] or tab >= shape [ 2 ] :
raise ValueError ( "Cell {value} outside of {shape}" . format ( value = value ... |
def _parse_error ( self , error ) :
"""Parses a single GLSL error and extracts the linenr and description
Other GLIR implementations may omit this .""" | error = str ( error )
# Nvidia
# 0(7 ) : error C1008 : undefined variable " MV "
m = re . match ( r'(\d+)\((\d+)\)\s*:\s(.*)' , error )
if m :
return int ( m . group ( 2 ) ) , m . group ( 3 )
# ATI / Intel
# ERROR : 0:131 : ' { ' : syntax error parse error
m = re . match ( r'ERROR:\s(\d+):(\d+):\s(.*)' , error )
if... |
def _split_section_and_key ( key ) :
"""Return a tuple with config section and key .""" | parts = key . split ( '.' )
if len ( parts ) > 1 :
return 'renku "{0}"' . format ( parts [ 0 ] ) , '.' . join ( parts [ 1 : ] )
return 'renku' , key |
def pexpireat ( self , key , timestamp ) :
"""Set expire timestamp on key , timestamp in milliseconds .
: raises TypeError : if timeout is not int""" | if not isinstance ( timestamp , int ) :
raise TypeError ( "timestamp argument must be int, not {!r}" . format ( timestamp ) )
fut = self . execute ( b'PEXPIREAT' , key , timestamp )
return wait_convert ( fut , bool ) |
def in_navitem ( self , resources , nav_href ) :
"""Given href of nav item , determine if resource is in it""" | # The navhref might end with ' / index ' so remove it if so
if nav_href . endswith ( '/index' ) :
nav_href = nav_href [ : - 6 ]
return self . docname . startswith ( nav_href ) |
def validate ( self , message , schema_name ) :
"""Validate a message given a schema .
Args :
message ( dict ) : Loaded JSON of pulled message from Google
PubSub .
schema _ name ( str ) : Name of schema to validate ` ` message ` `
against . ` ` schema _ name ` ` will be used to look up
schema from : py ... | err = None
try :
jsonschema . validate ( message , self . schemas [ schema_name ] )
except KeyError :
msg = ( f'Schema "{schema_name}" was not found (available: ' f'{", ".join(self.schemas.keys())})' )
err = { 'msg' : msg }
except jsonschema . ValidationError as e :
msg = ( f'Given message was not valid... |
def guess_feature_type ( nc , variable ) :
'''Returns a string describing the feature type for this variable
: param netCDF4 . Dataset nc : An open netCDF dataset
: param str variable : name of the variable to check''' | if is_point ( nc , variable ) :
return 'point'
if is_timeseries ( nc , variable ) :
return 'timeseries'
if is_multi_timeseries_orthogonal ( nc , variable ) :
return 'multi-timeseries-orthogonal'
if is_multi_timeseries_incomplete ( nc , variable ) :
return 'multi-timeseries-incomplete'
if is_cf_trajector... |
def resolveport ( self , definitions ) :
"""Resolve port _ type reference .
@ param definitions : A definitions object .
@ type definitions : L { Definitions }""" | ref = qualify ( self . type , self . root , definitions . tns )
port_type = definitions . port_types . get ( ref )
if port_type is None :
raise Exception ( "portType '%s', not-found" % self . type )
else :
self . type = port_type |
def value2rgba ( x : float , cmap : Callable = cm . RdYlGn , alpha_mult : float = 1.0 ) -> Tuple :
"Convert a value ` x ` from 0 to 1 ( inclusive ) to an RGBA tuple according to ` cmap ` times transparency ` alpha _ mult ` ." | c = cmap ( x )
rgb = ( np . array ( c [ : - 1 ] ) * 255 ) . astype ( int )
a = c [ - 1 ] * alpha_mult
return tuple ( rgb . tolist ( ) + [ a ] ) |
def has_legend ( self , bool_value ) :
"""Add , remove , or leave alone the ` ` < c : legend > ` ` child element depending
on current state and * bool _ value * . If * bool _ value * is | True | and no
` ` < c : legend > ` ` element is present , a new default element is added .
When | False | , any existing l... | if bool ( bool_value ) is False :
self . _remove_legend ( )
else :
if self . legend is None :
self . _add_legend ( ) |
def validate_introspect_request ( self , request ) :
"""Ensure the request is valid .
The protected resource calls the introspection endpoint using
an HTTP POST request with parameters sent as
" application / x - www - form - urlencoded " .
token REQUIRED . The string value of the token .
token _ type _ h... | self . _raise_on_missing_token ( request )
self . _raise_on_invalid_client ( request )
self . _raise_on_unsupported_token ( request ) |
def asm ( args ) :
"""% prog asm asmfile
Extract FASTA sequences from asm reads .""" | p = OptionParser ( asm . __doc__ )
opts , args = p . parse_args ( args )
if len ( args ) != 1 :
sys . exit ( p . print_help ( ) )
asmfile , = args
prefix = asmfile . rsplit ( "." , 1 ) [ 0 ]
ctgfastafile = prefix + ".ctg.fasta"
scffastafile = prefix + ".scf.fasta"
fp = open ( asmfile )
ctgfw = open ( ctgfastafile ,... |
def get_html ( self ) :
"""Bibliographic entry in html format .""" | # Author links
au_link = ( '<a href="https://www.scopus.com/authid/detail.url' '?origin=AuthorProfile&authorId={0}">{1}</a>' )
if len ( self . authors ) > 1 :
authors = u', ' . join ( [ au_link . format ( a . auid , a . given_name + ' ' + a . surname ) for a in self . authors [ 0 : - 1 ] ] )
authors += ( u' and... |
def parse ( self ) :
"""Executes the registered parsers to parse input configurations .""" | self . _config = _Config ( )
self . _setDefaults ( )
for parser in self . parsers :
for key , value in parser . parse ( self , self . _config ) . items ( ) :
key = self . _sanitizeName ( key )
if key not in self . configs :
raise UnknownConfigurationException ( key )
if value is ... |
def error_keys_not_found ( self , keys ) :
"""Check if the requested keys are found in the dict .
: param keys : keys to be looked for""" | try :
log . error ( "Filename: {0}" . format ( self [ 'meta' ] [ 'location' ] ) )
except :
log . error ( "Filename: {0}" . format ( self [ 'location' ] ) )
log . error ( "Key '{0}' does not exist" . format ( '.' . join ( keys ) ) )
indent = ""
last_index = len ( keys ) - 1
for i , k in enumerate ( keys ) :
... |
def reply_regexp ( self , user , regexp ) :
"""Prepares a trigger for the regular expression engine .
: param str user : The user ID invoking a reply .
: param str regexp : The original trigger text to be turned into a regexp .
: return regexp : The final regexp object .""" | if regexp in self . master . _regexc [ "trigger" ] : # Already compiled this one !
return self . master . _regexc [ "trigger" ] [ regexp ]
# If the trigger is simply ' * ' then the * there needs to become ( . * ? )
# to match the blank string too .
regexp = re . sub ( RE . zero_star , r'<zerowidthstar>' , regexp )
... |
def _set_lsp_frr_priority ( self , v , load = False ) :
"""Setter method for lsp _ frr _ priority , mapped from YANG variable / mpls _ config / router / mpls / mpls _ cmds _ holder / lsp / lsp _ frr / lsp _ frr _ priority ( container )
If this variable is read - only ( config : false ) in the
source YANG file ,... | if hasattr ( v , "_utype" ) :
v = v . _utype ( v )
try :
t = YANGDynClass ( v , base = lsp_frr_priority . lsp_frr_priority , is_container = 'container' , presence = False , yang_name = "lsp-frr-priority" , rest_name = "priority" , parent = self , path_helper = self . _path_helper , extmethods = self . _extmetho... |
def format_top ( counter , top = 3 ) :
"""Format a top .""" | items = islice ( reversed ( sorted ( counter . iteritems ( ) , key = lambda x : x [ 1 ] ) ) , 0 , top )
return u'; ' . join ( u'{g} ({nb})' . format ( g = g , nb = nb ) for g , nb in items ) |
def add_rec_new ( self , k , val ) :
"""Recursively add a new value and its children to me , and assign a
variable to it .
Args :
k ( str ) : The name of the variable to assign .
val ( LispVal ) : The value to be added and assigned .
Returns :
LispVal : The added value .""" | self . rec_new ( val )
self [ k ] = val
return val |
def set_start_location ( self , new_location ) : # type : ( int ) - > None
'''A method to set the location of the start of the partition .
Parameters :
new _ location - The new extent the UDF partition should start at .
Returns :
Nothing .''' | if not self . _initialized :
raise pycdlibexception . PyCdlibInternalError ( 'UDF Partition Volume Descriptor not initialized' )
self . part_start_location = new_location |
def _ensure_running ( name , no_start = False , path = None ) :
'''If the container is not currently running , start it . This function returns
the state that the container was in before changing
path
path to the container parent directory
default : / var / lib / lxc ( system )
. . versionadded : : 2015.8... | _ensure_exists ( name , path = path )
pre = state ( name , path = path )
if pre == 'running' : # This will be a no - op but running the function will give us a pretty
# return dict .
return start ( name , path = path )
elif pre == 'stopped' :
if no_start :
raise CommandExecutionError ( 'Container \'{0}\... |
def rerun ( version = "3.7.0" ) :
"""Rerun last example code block with specified version of python .""" | from commandlib import Command
Command ( DIR . gen . joinpath ( "py{0}" . format ( version ) , "bin" , "python" ) ) ( DIR . gen . joinpath ( "state" , "examplepythoncode.py" ) ) . in_dir ( DIR . gen . joinpath ( "state" ) ) . run ( ) |
def nucleotide_linkage ( residues ) :
"""Support for DNA / RNA ligands by finding missing covalent linkages to stitch DNA / RNA together .""" | nuc_covalent = [ ]
# Basic support for RNA / DNA as ligand #
nucleotides = [ 'A' , 'C' , 'T' , 'G' , 'U' , 'DA' , 'DC' , 'DT' , 'DG' , 'DU' ]
dna_rna = { }
# Dictionary of DNA / RNA residues by chain
covlinkage = namedtuple ( "covlinkage" , "id1 chain1 pos1 conf1 id2 chain2 pos2 conf2" )
# Create missing covlinkage ent... |
def AddNewSignature ( self , pattern , offset = None ) :
"""Adds a signature .
Args :
pattern ( bytes ) : pattern of the signature .
offset ( int ) : offset of the signature . None is used to indicate
the signature has no offset . A positive offset is relative from
the start of the data a negative offset ... | self . signatures . append ( Signature ( pattern , offset = offset ) ) |
def get_all_tags_of_reminder ( self , reminder_id ) :
"""Get all tags of reminder
This will iterate over all pages until it gets all elements .
So if the rate limit exceeded it will throw an Exception and you will get nothing
: param reminder _ id : the reminder id
: return : list""" | return self . _iterate_through_pages ( get_function = self . get_tags_of_reminder_per_page , resource = REMINDER_TAGS , ** { 'reminder_id' : reminder_id } ) |
def condition_yaw ( heading , relative = False ) :
"""Send MAV _ CMD _ CONDITION _ YAW message to point vehicle at a specified heading ( in degrees ) .
This method sets an absolute heading by default , but you can set the ` relative ` parameter
to ` True ` to set yaw relative to the current yaw heading .
By d... | if relative :
is_relative = 1
# yaw relative to direction of travel
else :
is_relative = 0
# yaw is an absolute angle
# create the CONDITION _ YAW command using command _ long _ encode ( )
msg = vehicle . message_factory . command_long_encode ( 0 , 0 , # target system , target component
mavutil . mavlin... |
def get_events ( self , from_ = None , to = None ) :
"""Query a slice of the events .
Events are always returned in the order the were added .
It also queries older event archives until it finds the event UUIDs
necessary .
Parameters :
from _ - - if not None , return only events added after the event with... | if from_ :
frombatchno = self . _find_batch_containing_event ( from_ )
if frombatchno is None :
msg = 'from_={0}' . format ( from_ )
raise EventStore . EventKeyDoesNotExistError ( msg )
else :
frombatchno = 0
if to :
tobatchno = self . _find_batch_containing_event ( to )
if tobatchno... |
def send ( self , topic , kmsg ) :
"""Send the message into the given topic
: param str topic : a kafka topic
: param ksr . transport . Message kmsg : Message to serialize
: return : Execution result
: rtype : kser . result . Result""" | try :
self . client . do_request ( method = "POST" , params = dict ( format = "raw" ) , path = "/topic/{}" . format ( topic ) , data = kmsg . MARSHMALLOW_SCHEMA . dump ( kmsg ) )
result = Result ( uuid = kmsg . uuid , stdout = "Message sent: {} ({})" . format ( kmsg . uuid , kmsg . entrypoint ) )
except Excepti... |
def _create_one ( self , ctx ) :
"""Creates an instance to be saved when a model is created .""" | assert isinstance ( ctx , ResourceQueryContext )
fields = dict_pick ( ctx . data , self . _model_columns )
model = self . model_cls ( ** fields )
return model |
def _respawn ( self ) :
"""Pick a random location for the star making sure it does
not overwrite an existing piece of text .""" | self . _cycle = randint ( 0 , len ( self . _star_chars ) )
( height , width ) = self . _screen . dimensions
while True :
self . _x = randint ( 0 , width - 1 )
self . _y = self . _screen . start_line + randint ( 0 , height - 1 )
if self . _screen . get_from ( self . _x , self . _y ) [ 0 ] == 32 :
bre... |
def isotopePattern ( sum_formula , threshold = 1e-4 , rel_threshold = True , desired_prob = None ) :
"""Calculates isotopic peaks for a sum formula .
: param sum _ formula : text representation of an atomic composition
: type sum _ formula : str
: param threshold : minimum peak abundance
: type threshold : ... | assert threshold >= 0 and threshold < 1
assert desired_prob is None or ( desired_prob > 0 and desired_prob <= 1 )
if desired_prob :
s = ims . spectrum_new_from_sf ( sum_formula . encode ( 'ascii' ) , desired_prob )
else :
s = ims . spectrum_new_from_sf_thr ( sum_formula . encode ( 'ascii' ) , threshold , rel_th... |
def build_extension ( extensions : Sequence [ ExtensionHeader ] ) -> str :
"""Unparse a ` ` Sec - WebSocket - Extensions ` ` header .
This is the reverse of : func : ` parse _ extension ` .""" | return ", " . join ( build_extension_item ( name , parameters ) for name , parameters in extensions ) |
def configBorderRouter ( self , P_Prefix , P_stable = 1 , P_default = 1 , P_slaac_preferred = 0 , P_Dhcp = 0 , P_preference = 0 , P_on_mesh = 1 , P_nd_dns = 0 ) :
"""configure the border router with a given prefix entry parameters
Args :
P _ Prefix : IPv6 prefix that is available on the Thread Network
P _ sta... | print '%s call configBorderRouter' % self . port
prefix = self . __convertIp6PrefixStringToIp6Address ( str ( P_Prefix ) )
print prefix
try :
parameter = ''
if P_slaac_preferred == 1 :
parameter += ' -a -f'
if P_stable == 1 :
parameter += ' -s'
if P_default == 1 :
parameter += ' ... |
def sentence ( random = random , * args , ** kwargs ) :
"""Return a whole sentence
> > > mock _ random . seed ( 0)
> > > sentence ( random = mock _ random )
" Agatha Incrediblebritches can ' t wait to smell two chimps in Boatbencheston . "
> > > mock _ random . seed ( 2)
> > > sentence ( random = mock _ r... | if 'name' in kwargs and kwargs [ 'name' ] :
nm = kwargs ( name )
elif random . choice ( [ True , False , False ] ) :
nm = name ( capitalize = True , random = random )
else :
nm = random . choice ( people )
def type_one ( ) :
return "{name} will {verb} {thing}." . format ( name = nm , verb = verb ( rando... |
def _execute_connector ( connector_command , top_level_argument , * file_contents , listing = None ) :
"""Executes a connector by executing the given connector _ command . The content of args will be the content of the
files handed to the connector cli .
: param connector _ command : The connector command to ex... | # create temp _ files for every file _ content
temp_files = [ ]
for file_content in file_contents :
if file_content is None :
continue
tmp_file = tempfile . NamedTemporaryFile ( 'w' )
json . dump ( file_content , tmp_file )
tmp_file . flush ( )
temp_files . append ( tmp_file )
tmp_listing_fi... |
def compute_payload_block_hash ( this ) :
"""Compute hash of each payload block .
Used to prevent payload corruption and tampering .""" | return hmac . new ( hashlib . sha512 ( struct . pack ( '<Q' , this . _index ) + hashlib . sha512 ( this . _ . _ . header . value . dynamic_header . master_seed . data + this . _ . transformed_key + b'\x01' ) . digest ( ) ) . digest ( ) , struct . pack ( '<Q' , this . _index ) + struct . pack ( '<I' , len ( this . block... |
async def shutdown ( self , container , force = False ) :
'''Shutdown all connections . Exclusive connections created by get _ connection will shutdown after release ( )''' | p = self . _connpool
self . _connpool = [ ]
self . _shutdown = True
if self . _defaultconn :
p . append ( self . _defaultconn )
self . _defaultconn = None
if self . _subscribeconn :
p . append ( self . _subscribeconn )
self . _subscribeconn = None
await container . execute_all ( [ self . _shutdown_conn ... |
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