signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def step ( self , x ) :
r"""perform a single Brownian dynamics step""" | return x - self . coeff_A * self . gradient ( x ) + self . coeff_B * np . random . normal ( size = self . dim ) |
def execute_sql ( server_context , schema_name , sql , container_path = None , max_rows = None , sort = None , offset = None , container_filter = None , save_in_session = None , parameters = None , required_version = None , timeout = _default_timeout ) :
"""Execute sql query against a LabKey server .
: param serv... | url = server_context . build_url ( 'query' , 'executeSql.api' , container_path = container_path )
payload = { 'schemaName' : schema_name , 'sql' : sql }
if container_filter is not None :
payload [ 'containerFilter' ] = container_filter
if max_rows is not None :
payload [ 'maxRows' ] = max_rows
if offset is not ... |
def _generate_request ( self , callname , request ) :
"""Generate a request object for delivery to the API""" | # Retrieve path from API class
schema = self . api . request_schema ( )
schema . context [ 'callname' ] = callname
return schema . dump ( request ) . data . get ( "payload" ) |
def _create_response_record ( self , response ) :
"""Creates record for lexicon API calls""" | record = dict ( )
record [ 'id' ] = response [ 'id' ]
record [ 'type' ] = response [ 'type' ]
record [ 'name' ] = self . _full_name ( response [ 'name' ] )
if 'content' in response :
record [ 'content' ] = response [ 'content' ] or ""
if 'ttl' in response :
record [ 'ttl' ] = response [ 'ttl' ]
if 'prio' in res... |
def _get_from_java_home ( self ) :
"""Retrieves the Java library path according to the JAVA _ HOME environment
variable
: return : The path to the JVM library , or None""" | # Get the environment variable
java_home = os . getenv ( "JAVA_HOME" )
if java_home and os . path . exists ( java_home ) : # Get the real installation path
java_home = os . path . realpath ( java_home )
# Cygwin has a bug in realpath
if not os . path . exists ( java_home ) :
java_home = os . getenv ... |
def changelog_file_option_validator ( ctx , param , value ) :
"""Checks that the given file path exists in the current working directory .
Returns a : class : ` ~ pathlib . Path ` object . If the file does not exist raises
a : class : ` ~ click . UsageError ` exception .""" | path = Path ( value )
if not path . exists ( ) :
filename = click . style ( path . name , fg = "blue" , bold = True )
ctx . fail ( "\n" f" {x_mark} Unable to find {filename}\n" ' Run "$ brau init" to create one' )
return path |
def search_worker ( self , regex , directory_path , names , binary = False , callback = None ) :
"""build a DirectoryResult for the given regex , directory path , and file names""" | try :
result = DirectoryResult ( directory_path )
def find_matches ( name ) :
full_path = path . join ( directory_path , name )
file_contents = get_file_contents ( full_path , binary )
start = 0
match = regex . search ( file_contents , start )
while match :
re... |
def indexbox ( msg = "Shall I continue?" , title = " " , choices = ( "Yes" , "No" ) , image = None ) :
"""Display a buttonbox with the specified choices .
Return the index of the choice selected .""" | reply = buttonbox ( msg = msg , choices = choices , title = title , image = image )
index = - 1
for choice in choices :
index = index + 1
if reply == choice :
return index
raise AssertionError ( "There is a program logic error in the EasyGui code for indexbox." ) |
def multi_p_run ( tot_num , _func , worker , params , n_process ) :
"""Run _ func with multi - process using params .""" | from multiprocessing import Process , Queue
out_q = Queue ( )
procs = [ ]
split_num = split_seq ( list ( range ( 0 , tot_num ) ) , n_process )
print ( tot_num , ">>" , split_num )
split_len = len ( split_num )
if n_process > split_len :
n_process = split_len
for i in range ( n_process ) :
_p = Process ( target ... |
def present ( name , level , devices , ** kwargs ) :
'''Verify that the raid is present
. . versionchanged : : 2014.7.0
name
The name of raid device to be created
level
The RAID level to use when creating the raid .
devices
A list of devices used to build the array .
kwargs
Optional arguments to b... | ret = { 'changes' : { } , 'comment' : '' , 'name' : name , 'result' : True }
# Device exists
raids = __salt__ [ 'raid.list' ] ( )
present = raids . get ( name )
# Decide whether to create or assemble
missing = [ ]
uuid_dict = { }
new_devices = [ ]
for dev in devices :
if dev == 'missing' or not __salt__ [ 'file.acc... |
def merge_equal_neighbors ( self ) :
"""Merge neighbors with same speaker .""" | IDX_LENGTH = 3
merged = self . segs . copy ( )
current_start = 0
j = 0
seg = self . segs . iloc [ 0 ]
for i in range ( 1 , self . num_segments ) :
seg = self . segs . iloc [ i ]
last = self . segs . iloc [ i - 1 ]
if seg . speaker == last . speaker :
merged . iat [ j , IDX_LENGTH ] = seg . start + s... |
def _handle_start_node ( self , attrs ) :
"""Handle opening node element
: param attrs : Attributes of the element
: type attrs : Dict""" | self . _curr = { 'attributes' : dict ( attrs ) , 'lat' : None , 'lon' : None , 'node_id' : None , 'tags' : { } }
if attrs . get ( 'id' , None ) is not None :
self . _curr [ 'node_id' ] = int ( attrs [ 'id' ] )
del self . _curr [ 'attributes' ] [ 'id' ]
if attrs . get ( 'lat' , None ) is not None :
self . _c... |
def _from_frame ( cls , frame ) :
"Copy constructor" | assert frame . _framespec == cls . _framespec
new = cls ( flags = frame . flags , frameno = frame . frameno )
for spec in cls . _framespec :
setattr ( new , spec . name , getattr ( frame , spec . name , None ) )
return new |
def delete_where_user_id ( cls , user_id ) :
"""delete by email""" | result = cls . where_user_id ( user_id )
if result is None :
return None
result . delete ( )
return True |
def parse_GPL ( filepath , entry_name = None , partial = None ) :
"""Parse GPL entry from SOFT file .
Args :
filepath ( : obj : ` str ` or : obj : ` Iterable ` ) : Path to file with 1 GPL entry
or list of lines representing GPL from GSE file .
entry _ name ( : obj : ` str ` , optional ) : Name of the entry ... | gsms = { }
gses = { }
gpl_soft = [ ]
has_table = False
gpl_name = entry_name
database = None
if isinstance ( filepath , str ) :
with utils . smart_open ( filepath ) as soft :
groupper = groupby ( soft , lambda x : x . startswith ( "^" ) )
for is_new_entry , group in groupper :
if is_new_... |
def download ( link , outdir = '.' , chunk_size = 4096 ) :
'''This is the Main function , which downloads a given link
and saves on outdir ( default = current directory )''' | url = None
fh = None
eta = 'unknown '
bytes_so_far = 0
filename = filename_from_url ( link ) or "."
cj = cjar . CookieJar ( )
# get filename for temp file in current directory
( fd_tmp , tmpfile ) = tempfile . mkstemp ( ".tmp" , prefix = filename + "." , dir = outdir )
os . close ( fd_tmp )
os . unlink ( tmpfile )
try ... |
def _get_criteria_matching_disks ( logical_disk , physical_drives ) :
"""Finds the physical drives matching the criteria of logical disk .
This method finds the physical drives matching the criteria
of the logical disk passed .
: param logical _ disk : The logical disk dictionary from raid config
: param ph... | matching_physical_drives = [ ]
criteria_to_consider = [ x for x in FILTER_CRITERIA if x in logical_disk ]
for physical_drive_object in physical_drives :
for criteria in criteria_to_consider :
logical_drive_value = logical_disk . get ( criteria )
physical_drive_value = getattr ( physical_drive_object... |
def add_optionals ( self , optionals_in , optionals_out ) :
"""Add optional inputs and outputs to the model spec .
Parameters
optionals _ in : [ str ]
List of inputs that are optionals .
optionals _ out : [ str ]
List of outputs that are optionals .
See Also
set _ input , set _ output""" | spec = self . spec
if ( not optionals_in ) and ( not optionals_out ) :
return
# assuming single sizes here
input_types = [ datatypes . Array ( dim ) for ( name , dim ) in optionals_in ]
output_types = [ datatypes . Array ( dim ) for ( name , dim ) in optionals_out ]
input_names = [ str ( name ) for ( name , dim ) i... |
def _build ( self , inputs , prev_state ) :
"""Connects the GRU module into the graph .
If this is not the first time the module has been connected to the graph ,
the Tensors provided as inputs and state must have the same final
dimension , in order for the existing variables to be the correct size for
thei... | input_size = inputs . get_shape ( ) [ 1 ]
weight_shape = ( input_size , self . _hidden_size )
u_shape = ( self . _hidden_size , self . _hidden_size )
bias_shape = ( self . _hidden_size , )
self . _wz = tf . get_variable ( GRU . WZ , weight_shape , dtype = inputs . dtype , initializer = self . _initializers . get ( GRU ... |
def authenticate ( self , username = None , password = None , ** kwargs ) :
"""" username " being passed is really email address and being compared to as such .""" | try :
user = User . objects . get ( email = username )
if user . check_password ( password ) :
return user
except ( User . DoesNotExist , User . MultipleObjectsReturned ) :
logging . warning ( 'Unsuccessful login attempt using username/email: {0}' . format ( username ) )
return None |
def _format_data ( self , data , charset ) :
"""Format data into XML .""" | if data is None or data == '' :
return u''
stream = StringIO . StringIO ( )
xml = SimplerXMLGenerator ( stream , charset )
xml . startDocument ( )
xml . startElement ( self . _root_element_name ( ) , { } )
self . _to_xml ( xml , data )
xml . endElement ( self . _root_element_name ( ) )
xml . endDocument ( )
return ... |
def match_rules ( tree , rules , fun = None , multi = False ) :
"""Matches a Tree structure with the given query rules .
Query rules are represented as a dictionary of template to action .
Action is either a function , or a dictionary of subtemplate parameter to rules : :
rules = { ' template ' : { ' key ' : ... | if multi :
context = match_rules_context_multi ( tree , rules )
else :
context = match_rules_context ( tree , rules )
if not context :
return None
if fun :
args = fun . __code__ . co_varnames
if multi :
res = [ ]
for c in context :
action_context = { }
... |
def download ( url , params = None , accept = "xml" , ** kwds ) :
"""Helper function to download a file and return its content .
Parameters
url : string
The URL to be parsed .
params : dict ( optional )
Dictionary containing query parameters . For required keys
and accepted values see e . g .
https : ... | # Value check
accepted = ( "json" , "xml" , "atom+xml" )
if accept . lower ( ) not in accepted :
raise ValueError ( 'accept parameter must be one of ' + ', ' . join ( accepted ) )
# Get credentials
key = config . get ( 'Authentication' , 'APIKey' )
header = { 'X-ELS-APIKey' : key }
if config . has_option ( 'Authent... |
def removeClass ( self , * classes : str ) -> None :
"""[ Not Standard ] Remove classes from this node .""" | _remove_cl = [ ]
for class_ in classes :
if class_ not in self . classList :
if class_ in self . get_class_list ( ) :
logger . warning ( 'tried to remove class-level class: ' '{}' . format ( class_ ) )
else :
logger . warning ( 'tried to remove non-existing class: {}' . forma... |
def Run ( self , args ) :
"""Run .""" | # Open the file .
fd = vfs . VFSOpen ( args . pathspec , progress_callback = self . Progress )
if args . address_family == rdf_client_network . NetworkAddress . Family . INET :
family = socket . AF_INET
elif args . address_family == rdf_client_network . NetworkAddress . Family . INET6 :
family = socket . AF_INE... |
def get_obj ( self , objpath , metahash , dst_path ) :
"""Get object from cache , write it to dst _ path .
Args :
objpath : filename relative to buildroot
( example : mini - boot / blahblah / somefile . bin )
metahash : metahash . See targets / base . py
dst _ path : Absolute path where the file should be... | incachepath = self . path_in_cache ( objpath , metahash )
if not os . path . exists ( incachepath ) :
raise CacheMiss ( '%s not in cache.' % incachepath )
else :
log . debug ( 'Cache hit! %s~%s' , objpath , metahash . hexdigest ( ) )
if not os . path . exists ( os . path . dirname ( dst_path ) ) :
o... |
def eeg_to_df ( eeg , index = None , include = "all" , exclude = None , hemisphere = "both" , central = True ) :
"""Convert mne Raw or Epochs object to dataframe or dict of dataframes .
DOCS INCOMPLETE : (""" | if isinstance ( eeg , mne . Epochs ) :
data = { }
if index is None :
index = range ( len ( eeg ) )
for epoch_index , epoch in zip ( index , eeg . get_data ( ) ) :
epoch = pd . DataFrame ( epoch . T )
epoch . columns = eeg . ch_names
epoch . index = eeg . times
selecti... |
def search_for_vcs ( self , dependency ) : # type : ( VCSDependency ) - > List [ Package ]
"""Search for the specifications that match the given VCS dependency .
Basically , we clone the repository in a temporary directory
and get the information we need by checking out the specified reference .""" | if dependency . vcs != "git" :
raise ValueError ( "Unsupported VCS dependency {}" . format ( dependency . vcs ) )
tmp_dir = Path ( mkdtemp ( prefix = "pypoetry-git-{}" . format ( dependency . name ) ) )
try :
git = Git ( )
git . clone ( dependency . source , tmp_dir )
git . checkout ( dependency . refer... |
def occurs_in_type ( v , type2 ) :
"""Checks whether a type variable occurs in a type expression .
Note : Must be called with v pre - pruned
Args :
v : The TypeVariable to be tested for
type2 : The type in which to search
Returns :
True if v occurs in type2 , otherwise False""" | pruned_type2 = prune ( type2 )
if pruned_type2 == v :
return True
elif isinstance ( pruned_type2 , TypeOperator ) :
return occurs_in ( v , pruned_type2 . types )
return False |
def expectScreen ( self , filename , maxrms = 0 ) :
"""Wait until the display matches a target image
filename : an image file to read and compare against
maxrms : the maximum root mean square between histograms of the
screen and target image""" | log . debug ( 'expectScreen %s' , filename )
return self . _expectFramebuffer ( filename , 0 , 0 , maxrms ) |
def intermediate_cpfs ( self ) -> List [ CPF ] :
'''Returns list of intermediate - fluent CPFs in level order .''' | _ , cpfs = self . cpfs
interm_cpfs = [ cpf for cpf in cpfs if cpf . name in self . intermediate_fluents ]
interm_cpfs = sorted ( interm_cpfs , key = lambda cpf : ( self . intermediate_fluents [ cpf . name ] . level , cpf . name ) )
return interm_cpfs |
def _json_to_subscriptions ( response_body ) :
"""Returns a list of Subscription objects""" | data = json . loads ( response_body )
subscriptions = [ ]
for subscription_data in data . get ( "subscriptionList" , [ ] ) :
subscriptions . append ( Subscription ( ) . from_json ( data . get ( 'uwNetID' ) , subscription_data ) )
return subscriptions |
def validate ( self , value , validator ) :
"""Validates and returns the value .
If the value does not validate against the schema , SchemaValidationError
will be raised .
: param value : A value to validate ( usually a dict ) .
: param validator : An instance of a jsonschema validator class , as
created ... | try :
validator . validate ( value )
except Exception as e :
logging . debug ( e , exc_info = e )
if isinstance ( e , DoctorError ) :
raise
else : # Gather all the validation errors
validation_errors = sorted ( validator . iter_errors ( value ) , key = lambda e : e . path )
error... |
def dbus_readBytesTwoFDs ( self , fd1 , fd2 , byte_count ) :
"""Reads byte _ count from fd1 and fd2 . Returns concatenation .""" | result = bytearray ( )
for fd in ( fd1 , fd2 ) :
f = os . fdopen ( fd , 'rb' )
result . extend ( f . read ( byte_count ) )
f . close ( )
return result |
def speziale_grun ( v , v0 , gamma0 , q0 , q1 ) :
"""calculate Gruneisen parameter for the Speziale equation
: param v : unit - cell volume in A ^ 3
: param v0 : unit - cell volume in A ^ 3 at 1 bar
: param gamma0 : Gruneisen parameter at 1 bar
: param q0 : logarithmic derivative of Gruneisen parameter
: ... | if isuncertainties ( [ v , v0 , gamma0 , q0 , q1 ] ) :
gamma = gamma0 * unp . exp ( q0 / q1 * ( ( v / v0 ) ** q1 - 1. ) )
else :
gamma = gamma0 * np . exp ( q0 / q1 * ( ( v / v0 ) ** q1 - 1. ) )
return gamma |
def scrape_wikinews ( conn , project , articleset , query ) :
"""Scrape wikinews articles from the given query
@ param conn : The AmcatAPI object
@ param articleset : The target articleset ID
@ param category : The wikinews category name""" | url = "http://en.wikinews.org/w/index.php?search={}&limit=50" . format ( query )
logging . info ( url )
for page in get_pages ( url ) :
urls = get_article_urls ( page )
arts = list ( get_articles ( urls ) )
logging . info ( "Adding {} articles to set {}:{}" . format ( len ( arts ) , project , articleset ) )... |
def wait_for_n_keypresses ( self , key , n = 1 ) :
"""Waits till one key was pressed n times .
: param key : the key to be pressed as defined by pygame . E . g .
pygame . K _ LEFT for the left arrow key
: type key : int
: param n : number of repetitions till the function returns
: type n : int""" | my_const = "key_consumed"
counter = 0
def keypress_listener ( e ) :
return my_const if e . type == pygame . KEYDOWN and e . key == key else EventConsumerInfo . DONT_CARE
while counter < n :
if self . listen ( keypress_listener ) == my_const :
counter += 1 |
def get_current_transport_info ( self ) :
"""Get the current playback state .
Returns :
dict : The following information about the
speaker ' s playing state :
* current _ transport _ state ( ` ` PLAYING ` ` , ` ` TRANSITIONING ` ` ,
` ` PAUSED _ PLAYBACK ` ` , ` ` STOPPED ` ` )
* current _ transport _ s... | response = self . avTransport . GetTransportInfo ( [ ( 'InstanceID' , 0 ) , ] )
playstate = { 'current_transport_status' : '' , 'current_transport_state' : '' , 'current_transport_speed' : '' }
playstate [ 'current_transport_state' ] = response [ 'CurrentTransportState' ]
playstate [ 'current_transport_status' ] = resp... |
def max_interval_intersec ( S ) :
"""determine a value that is contained in a largest number of given intervals
: param S : list of half open intervals
: complexity : O ( n log n ) , where n = len ( S )""" | B = ( [ ( left , + 1 ) for left , right in S ] + [ ( right , - 1 ) for left , right in S ] )
B . sort ( )
c = 0
best = ( c , None )
for x , d in B :
c += d
if best [ 0 ] < c :
best = ( c , x )
return best |
def null_space ( M , k , k_skip = 1 , eigen_solver = 'arpack' , random_state = None , solver_kwds = None ) :
"""Find the null space of a matrix M : eigenvectors associated with 0 eigenvalues
Parameters
M : { array , matrix , sparse matrix , LinearOperator }
Input covariance matrix : should be symmetric positi... | eigen_solver , solver_kwds = check_eigen_solver ( eigen_solver , solver_kwds , size = M . shape [ 0 ] , nvec = k + k_skip )
random_state = check_random_state ( random_state )
if eigen_solver == 'arpack' : # This matches the internal initial state used by ARPACK
v0 = random_state . uniform ( - 1 , 1 , M . shape [ 0 ... |
def txn_storeAssociation ( self , server_url , association ) :
"""Set the association for the server URL .
Association - > NoneType""" | a = association
self . db_set_assoc ( server_url , a . handle , self . blobEncode ( a . secret ) , a . issued , a . lifetime , a . assoc_type ) |
def do_p ( self , arg ) :
"""p expression
Print the value of the expression .""" | try :
self . message ( bdb . safe_repr ( self . _getval ( arg ) ) )
except Exception :
pass |
async def download_file ( self , file_path : base . String , destination : Optional [ base . InputFile ] = None , timeout : Optional [ base . Integer ] = sentinel , chunk_size : Optional [ base . Integer ] = 65536 , seek : Optional [ base . Boolean ] = True ) -> Union [ io . BytesIO , io . FileIO ] :
"""Download fi... | if destination is None :
destination = io . BytesIO ( )
url = api . Methods . file_url ( token = self . __token , path = file_path )
dest = destination if isinstance ( destination , io . IOBase ) else open ( destination , 'wb' )
async with self . session . get ( url , timeout = timeout , proxy = self . proxy , prox... |
def plot_rank ( data , var_names = None , coords = None , bins = None , ref_line = True , figsize = None , axes = None ) :
"""Plot rank order statistics of chains .
From the paper : Rank plots are histograms of the ranked posterior
draws ( ranked over all chains ) plotted separately for each chain .
If all of... | posterior_data = convert_to_dataset ( data , group = "posterior" )
if coords is not None :
posterior_data = posterior_data . sel ( ** coords )
var_names = _var_names ( var_names , posterior_data )
plotters = list ( xarray_var_iter ( posterior_data , var_names = var_names , combined = True ) )
if bins is None : # Us... |
def flush ( self ) :
"""Commit backing storage to disk
This method is largely internal , and it is not necessary to call this
from user code . It should not be explicitly invoked and may be removed
in future versions .""" | if self . kind == TraceField :
self . filehandle . putth ( self . traceno , self . buf )
elif self . kind == BinField :
self . filehandle . putbin ( self . buf )
else :
msg = 'Object corrupted: kind {} not valid'
raise RuntimeError ( msg . format ( self . kind ) ) |
def content_break ( self , el ) :
"""Break on specified boundaries .""" | should_break = False
if self . type == 'odp' :
if el . name == 'page' and el . namespace and el . namespace == self . namespaces [ 'draw' ] :
should_break = True
return should_break |
def parse ( some_text , ** kwargs ) :
"""Creates request to AddressParser
and returns list of Address objects""" | ap = parser . AddressParser ( ** kwargs )
return ap . parse ( some_text ) |
def get ( cls , xuid , scid , clip_id ) :
'''Gets a specific game clip
: param xuid : xuid of an xbox live user
: param scid : scid of a clip
: param clip _ id : id of a clip''' | url = ( 'https://gameclipsmetadata.xboxlive.com/users' '/xuid(%(xuid)s)/scids/%(scid)s/clips/%(clip_id)s' % { 'xuid' : xuid , 'scid' : scid , 'clip_id' : clip_id , } )
resp = xbox . client . _get ( url )
# scid does not seem to matter when fetching clips ,
# as long as it looks like a uuid it should be fine .
# perhaps... |
def getPID ( self ) :
"""Returns the PID for the associated app
( or - 1 , if no app is associated or the app is not running )""" | if self . _pid is not None :
if not PlatformManager . isPIDValid ( self . _pid ) :
self . _pid = - 1
return self . _pid
return - 1 |
def update ( self , * , name = None , position = None , visibility = None ) :
"""Changes the name , position or visibility of this worksheet""" | if name is None and position is None and visibility is None :
raise ValueError ( 'Provide at least one parameter to update' )
data = { }
if name :
data [ 'name' ] = name
if position :
data [ 'position' ] = position
if visibility :
data [ 'visibility' ] = visibility
response = self . session . patch ( se... |
def _get_rs_id ( variant , rs_map , variant_type ) :
"""Given a variant dict , return unambiguous RS ID
TODO
Some sequence alterations appear to have mappings to dbsnp ' s notation
for example ,
reference allele : TTTTT
variant allele : TTTTT
Is theoretically the same as - / T , we should clarify with U... | rs_id = None
if variant_type == 'snp' :
variant_key = "{0}-{1}" . format ( variant [ 'chromosome' ] , variant [ 'position' ] )
if variant_key in rs_map :
snp_candidates = [ rs_dict for rs_dict in rs_map [ variant_key ] if rs_dict [ 'type' ] == 'snp' ]
if len ( snp_candidates ) == 1 :
... |
def set_key ( key , value , host = None , port = None , db = None , password = None ) :
'''Set redis key value
CLI Example :
. . code - block : : bash
salt ' * ' redis . set _ key foo bar''' | server = _connect ( host , port , db , password )
return server . set ( key , value ) |
def eagle ( args ) :
"""% prog eagle fastafile""" | p = OptionParser ( eagle . __doc__ )
p . add_option ( "--share" , default = "/usr/local/share/EAGLE/" , help = "Default EAGLE share path" )
add_sim_options ( p )
opts , args = p . parse_args ( args )
if len ( args ) != 1 :
sys . exit ( not p . print_help ( ) )
fastafile , = args
share = opts . share
depth = opts . ... |
def read_config ( config_path = CONFIG_PATH ) :
"""Read the config information from the config file .
Args :
config _ path ( str ) : Relative path to the email config file .
Returns :
defaultdict : A defaultdict with the config information .
Raises :
IOError""" | if not os . path . isfile ( config_path ) :
raise IOError ( "No config file found at %s" % config_path )
config_parser = configparser . ConfigParser ( )
config_parser . read ( config_path )
config = _config_parser_to_defaultdict ( config_parser )
return config |
def search_pages ( self , page_ids = None , begin = 0 , count = 10 ) :
"""查询页面列表
详情请参考
http : / / mp . weixin . qq . com / wiki / 5/6626199ea8757c752046d8e46cf13251 . html
: param page _ ids : 指定页面的id列表
: param begin : 页面列表的起始索引值
: param count : 待查询的页面个数
: return : 页面查询结果信息""" | if not page_ids :
data = { 'type' : 2 , 'begin' : begin , 'count' : count }
else :
if not isinstance ( page_ids , ( tuple , list ) ) :
page_ids = [ page_ids ]
data = { 'type' : 1 , 'page_ids' : page_ids }
res = self . _post ( 'shakearound/page/search' , data = data , result_processor = lambda x : x ... |
def fpy_interface ( fpy , static , interface , typedict ) :
"""Splices the full list of subroutines and the module procedure list
into the static . f90 file .
: arg static : the string contents of the static . f90 file .
: arg interface : the name of the interface * field * being replaced .
: arg typedict :... | modprocs = [ ]
subtext = [ ]
for dtype , combos in list ( typedict . items ( ) ) :
for tcombo in combos :
kind , suffix = tcombo
xnames , sub = fpy_interface_sub ( fpy , dtype , kind , suffix )
modprocs . extend ( xnames )
subtext . append ( sub )
subtext . append ( "\n" )
# Next... |
def modifyInPlace ( self , * , sort = None , purge = False , done = None ) :
"""Like Model . modify , but changes existing database instead of
returning a new one .""" | self . data = self . modify ( sort = sort , purge = purge , done = done ) |
def _decimal_to_128 ( value ) :
"""Converts a decimal . Decimal to BID ( high bits , low bits ) .
: Parameters :
- ` value ` : An instance of decimal . Decimal""" | with decimal . localcontext ( _DEC128_CTX ) as ctx :
value = ctx . create_decimal ( value )
if value . is_infinite ( ) :
return _NINF if value . is_signed ( ) else _PINF
sign , digits , exponent = value . as_tuple ( )
if value . is_nan ( ) :
if digits :
raise ValueError ( "NaN with debug payload is ... |
def switch_to_table ( self , event ) :
"""Switches grid to table
Parameters
event . newtable : Integer
\t Table that the grid is switched to""" | newtable = event . newtable
no_tabs = self . grid . code_array . shape [ 2 ] - 1
if 0 <= newtable <= no_tabs :
self . grid . current_table = newtable
self . grid . SetToolTip ( None )
# Delete renderer cache
self . grid . grid_renderer . cell_cache . clear ( )
# Delete video cells
video_cells = ... |
def draw_scatter_plot ( world , size , target ) :
"""This function can be used on a generic canvas ( either an image to save
on disk or a canvas part of a GUI )""" | # Find min and max values of humidity and temperature on land so we can
# normalize temperature and humidity to the chart
humid = numpy . ma . masked_array ( world . layers [ 'humidity' ] . data , mask = world . layers [ 'ocean' ] . data )
temp = numpy . ma . masked_array ( world . layers [ 'temperature' ] . data , mas... |
def string ( self , * args ) :
"""return string stored in node""" | data = self . bytes ( * args )
if data is not None :
return data . rstrip ( b"\x00" ) . decode ( 'utf-8' ) |
def wrap_text ( paragraph , line_count , min_char_per_line = 0 ) :
"""Wraps the given text to the specified number of lines .""" | one_string = strip_all_white_space ( paragraph )
if min_char_per_line :
lines = wrap ( one_string , width = min_char_per_line )
try :
return lines [ : line_count ]
except IndexError :
return lines
else :
return wrap ( one_string , len ( one_string ) / line_count ) |
def read_tb ( path ) :
"""path : a tensorboard file OR a directory , where we will find all TB files
of the form events . *""" | import pandas
import numpy as np
from glob import glob
from collections import defaultdict
import tensorflow as tf
if osp . isdir ( path ) :
fnames = glob ( osp . join ( path , "events.*" ) )
elif osp . basename ( path ) . startswith ( "events." ) :
fnames = [ path ]
else :
raise NotImplementedError ( "Expe... |
def _parse_doc ( doc = '' ) :
"""Parse a docstring into title and description .
Args
doc : str
A docstring , optionally with a title line , separated from a description
line by at least one blank line .
Returns
title : str
The first line of the docstring .
description : str
The rest of a docstring... | title , description = '' , ''
if doc :
sp = doc . split ( '\n' , 1 )
title = sp [ 0 ] . strip ( )
if len ( sp ) > 1 :
description = textwrap . dedent ( sp [ 1 ] ) . strip ( )
return ( title , description ) |
def authenticate ( self , auth_url = None , ** kwargs ) :
"""Authenticates a user via the Keystone Identity API .""" | LOG . debug ( 'Beginning user authentication' )
if not auth_url :
auth_url = settings . OPENSTACK_KEYSTONE_URL
auth_url , url_fixed = utils . fix_auth_url_version_prefix ( auth_url )
if url_fixed :
LOG . warning ( "The OPENSTACK_KEYSTONE_URL setting points to a v2.0 " "Keystone endpoint, but v3 is specified as ... |
def _pusher_connect_handler ( self , data ) :
"""Event handler for the connection _ established event . Binds the
shortlink _ scanned event""" | self . channel = self . pusher . subscribe ( self . pos_callback_chan )
for listener in self . pusher_connected_listeners :
listener ( data ) |
def _validate_json_for_global_workflow ( json_spec , args ) :
"""Validates fields used for building a global workflow .
Since building a global workflow is done after all the underlying workflows
are built , which may be time - consuming , we validate as much as possible here .""" | # TODO : verify the billTo can build the workflow
# TODO : if the global workflow build fails add an option to interactively change billto
# TODO : ( or other simple fields ) instead of failing altogether
# TODO : get a confirmation before building a workflow that may be costly
if 'name' not in json_spec :
raise Wo... |
def plot_roc_curve ( y_true , y_probas , title = 'ROC Curves' , curves = ( 'micro' , 'macro' , 'each_class' ) , ax = None , figsize = None , cmap = 'nipy_spectral' , title_fontsize = "large" , text_fontsize = "medium" ) :
"""Generates the ROC curves from labels and predicted scores / probabilities
Args :
y _ tr... | y_true = np . array ( y_true )
y_probas = np . array ( y_probas )
if 'micro' not in curves and 'macro' not in curves and 'each_class' not in curves :
raise ValueError ( 'Invalid argument for curves as it ' 'only takes "micro", "macro", or "each_class"' )
classes = np . unique ( y_true )
probas = y_probas
fpr = dict... |
def stdout_redirector ( ) :
"""Simplify redirect of stdout .
Taken from here : https : / / eli . thegreenplace . net / 2015 / redirecting - all - kinds - of - stdout - in - python /""" | old_stdout = sys . stdout
sys . stdout = Stream ( )
try :
yield sys . stdout
finally :
sys . stdout . close ( )
sys . stdout = old_stdout |
def _get_implied_apps ( self , detected_apps ) :
"""Get the set of apps implied by ` detected _ apps ` .""" | def __get_implied_apps ( apps ) :
_implied_apps = set ( )
for app in apps :
try :
_implied_apps . update ( set ( self . apps [ app ] [ 'implies' ] ) )
except KeyError :
pass
return _implied_apps
implied_apps = __get_implied_apps ( detected_apps )
all_implied_apps = se... |
def set_of_vars ( arg_plot ) :
"""Build set of needed variables .
Args :
arg _ plot ( str ) : string with variable names separated with ` ` , ` ` .
Returns :
set of str : set of variables .""" | return set ( var for var in arg_plot . split ( ',' ) if var in phyvars . PLATES ) |
def main ( ) -> None :
"""The main CLI interface entry point .""" | parser = argparse . ArgumentParser ( description = "Security analysis of Ethereum smart contracts" )
create_parser ( parser )
# Get config values
args = parser . parse_args ( )
parse_args ( parser = parser , args = args ) |
def get_point_index ( point , all_points , eps = 1e-4 ) :
"""Get the index of a point in an array""" | inds = np . where ( np . linalg . norm ( point - all_points , axis = 1 ) < eps )
if inds [ 0 ] . shape [ 0 ] == 0 :
return - 1
return inds [ 0 ] [ 0 ] |
def _m_to_e ( cls , e , M ) :
"""Conversion from Mean Anomaly to Eccentric anomaly
Procedures for solving Kepler ' s Equation , A . W . Odell and R . H . Gooding ,
Celestial Mechanics 38 ( 1986 ) 307-334""" | k1 = 3 * np . pi + 2
k2 = np . pi - 1
k3 = 6 * np . pi - 1
A = 3 * k2 ** 2 / k1
B = k3 ** 2 / ( 6 * k1 )
m1 = float ( M )
if abs ( m1 ) < 1 / 6 :
E = m1 + e * ( 6 * m1 ) ** ( 1 / 3 ) - m1
elif m1 < 0 :
w = np . pi + m1
E = m1 + e * ( A * w / ( B - w ) - np . pi - m1 )
else :
w = np . pi - m1
E = m1 ... |
def find_stages ( document ) :
"""Find * * stages * * in document .
Args :
document ( dict ) : validated spline document loaded from a yaml file .
Returns :
list : stages as a part of the spline document or an empty list if not given .
> > > find _ stages ( { ' pipeline ' : [ { ' stage ( Prepare ) ' : 1 }... | names = [ ]
if 'pipeline' in document :
for entry in document [ 'pipeline' ] : # each entry is dictionary with one key only
key , _ = list ( entry . items ( ) ) [ 0 ]
if key . startswith ( "stage(" ) :
names . append ( key . replace ( 'stage(' , '' ) . replace ( ')' , '' ) )
return names |
def batch_get ( self , offset = 0 , count = 50 , status_list = None ) :
"""批量查询卡券信息""" | card_data = { 'offset' : offset , 'count' : count }
if status_list :
card_data [ 'status_list' ] = status_list
return self . _post ( 'card/batchget' , data = card_data ) |
def pipecmd ( cmd1 , cmd2 ) :
"""Return output of " cmd1 | cmd2 " .""" | p1 = subprocess . Popen ( cmd1 , stdout = subprocess . PIPE )
p2 = subprocess . Popen ( cmd2 , stdin = p1 . stdout , stdout = subprocess . PIPE )
p1 . stdout . close ( )
# Allow p1 to receive a SIGPIPE if p2 exits .
return p2 . communicate ( ) [ 0 ] |
def apply_plugin_settings ( self , options ) :
"""Apply configuration file ' s plugin settings""" | font_n = 'plugin_font'
font_o = self . get_plugin_font ( )
help_n = 'connect_to_oi'
help_o = CONF . get ( 'help' , 'connect/ipython_console' )
color_scheme_n = 'color_scheme_name'
color_scheme_o = CONF . get ( 'appearance' , 'selected' )
show_time_n = 'show_elapsed_time'
show_time_o = self . get_option ( show_time_n )
... |
def accept ( self ) : # type : ( ) - > str
"""The content - type for the response to the client .
Returns :
( str ) : The value of the header ' Accept ' or the user - supplied SAGEMAKER _ DEFAULT _ INVOCATIONS _ ACCEPT
environment variable .""" | accept = self . headers . get ( 'Accept' )
if not accept or accept == _content_types . ANY :
return self . _default_accept
else :
return accept |
def reduce_to_2d ( arr ) :
"""Given a np . npdarray with nDims > 2 , reduce it to 2d .
It does this by selecting the zeroth coordinate for every dimension greater
than two .
Args :
arr : a numpy ndarray of dimension at least 2.
Returns :
A two - dimensional subarray from the input array .
Raises :
V... | if not isinstance ( arr , np . ndarray ) :
raise ValueError ( 'reduce_to_2d requires a numpy.ndarray' )
ndims = len ( arr . shape )
if ndims < 2 :
raise ValueError ( 'reduce_to_2d requires an array of dimensionality >=2' )
# slice ( None ) is equivalent to ` : ` , so we take arr [ 0,0 , . . . 0 , : , : ]
slices... |
def get_arguments ( ) :
"""Get parsed arguments .""" | parser = argparse . ArgumentParser ( "Lupupy: Command Line Utility" )
parser . add_argument ( '-u' , '--username' , help = 'Username' , required = False )
parser . add_argument ( '-p' , '--password' , help = 'Password' , required = False )
parser . add_argument ( '--arm' , help = 'Arm alarm to mode' , required = False ... |
async def update ( self ) :
"""Updates this interface ' s messages with the latest data .""" | if self . update_lock . locked ( ) :
return
async with self . update_lock :
if self . update_lock . locked ( ) : # if this engagement has caused the semaphore to exhaust ,
# we are overloaded and need to calm down .
await asyncio . sleep ( 1 )
if not self . message : # too fast , stagger so this... |
def validate_err_calc ( val ) :
"""Validation function for the
: attr : ` psy _ simple . plotter . FldmeanPlotter . err _ calc ` formatoption""" | try :
val = validate_float ( val )
except ( ValueError , TypeError ) :
pass
else :
if val <= 100 and val >= 0 :
return val
raise ValueError ( "Percentiles for the error calculation must lie " "between 0 and 100, not %s" % val )
try :
val = ValidateList ( float , 2 ) ( val )
except ( ValueErr... |
def check_regularizers ( regularizers , keys ) :
"""Checks the given regularizers .
This checks that ` regularizers ` is a dictionary that only contains keys in
` keys ` , and furthermore the entries in ` regularizers ` are functions or
further dictionaries ( the latter used , for example , in passing regular... | if regularizers is None :
return { }
_assert_is_dictlike ( regularizers , valid_keys = keys )
keys = set ( keys )
if not set ( regularizers ) <= keys :
extra_keys = set ( regularizers ) - keys
raise KeyError ( "Invalid regularizer keys {}, regularizers can only " "be provided for {}" . format ( ", " . join ... |
def get_player_img ( player_id ) :
"""Returns the image of the player from stats . nba . com as a numpy array and
saves the image as PNG file in the current directory .
Parameters
player _ id : int
The player ID used to find the image .
Returns
player _ img : ndarray
The multidimensional numpy array o... | url = "http://stats.nba.com/media/players/230x185/" + str ( player_id ) + ".png"
img_file = str ( player_id ) + ".png"
pic = urlretrieve ( url , img_file )
player_img = plt . imread ( pic [ 0 ] )
return player_img |
def prior ( self ) :
"""Model prior for particular model .
Product of eclipse probability ( ` ` self . prob ` ` ) ,
the fraction of scenario that is allowed by the various
constraints ( ` ` self . selectfrac ` ` ) , and all additional
factors in ` ` self . priorfactors ` ` .""" | prior = self . prob * self . selectfrac
for f in self . priorfactors :
prior *= self . priorfactors [ f ]
return prior |
def width_tuple ( value ) :
"""test if value is a valid width indicator ( for a sub - widget in a column ) .
This can either be
( ' fit ' , min , max ) : use the length actually needed for the content , padded
to use at least width min , and cut of at width max .
Here , min and max are positive integers or ... | if value is None :
res = 'fit' , 0 , 0
elif not isinstance ( value , ( list , tuple ) ) :
raise VdtTypeError ( value )
elif value [ 0 ] not in [ 'fit' , 'weight' ] :
raise VdtTypeError ( value )
if value [ 0 ] == 'fit' :
if not isinstance ( value [ 1 ] , int ) or not isinstance ( value [ 2 ] , int ) :
... |
def get_cluster_interfaces ( cluster , extra_cond = lambda nic : True ) :
"""Get the network interfaces names corresponding to a criteria .
Note that the cluster is passed ( not the individual node names ) , thus it is
assumed that all nodes in a cluster have the same interface names same
configuration . In a... | nics = get_nics ( cluster )
# NOTE ( msimonin ) : Since 05/18 nics on g5k nodes have predictable names but
# the api description keep the legacy name ( device key ) and the new
# predictable name ( key name ) . The legacy names is still used for api
# request to the vlan endpoint This should be fixed in
# https : / / i... |
def plt_goea_results ( fout_img , goea_results , ** kws ) :
"""Plot a single page .""" | go_sources = [ rec . GO for rec in goea_results ]
go2obj = { rec . GO : rec . goterm for rec in goea_results }
gosubdag = GoSubDag ( go_sources , go2obj , rcntobj = True )
godagplot = GoSubDagPlot ( gosubdag , goea_results = goea_results , ** kws )
godagplot . plt_dag ( fout_img ) |
def read_text ( self ) : # type : ( ) - > Dict [ str , str ]
"""Get version out of ad - hoc version . txt
: return :""" | found = { }
for file in self . file_inventory . text_files :
if not os . path . isfile ( file ) :
continue
with self . file_opener . open_this ( file , "r" ) as infile :
text = infile . readline ( )
found [ file ] = text . strip ( " \n" )
return found |
def parse_security_group ( self , global_params , region , security_group ) :
"""Parse a single Redsfhit security group
: param global _ params : Parameters shared for all regions
: param region : Name of the AWS region
: param security ) _ group : Security group""" | name = security_group . pop ( 'ClusterSecurityGroupName' )
security_group [ 'name' ] = name
self . security_groups [ 'name' ] = security_group |
def disable_svc_notifications ( self , service ) :
"""Disable notifications for a service
Format of the line that triggers function call : :
DISABLE _ SVC _ NOTIFICATIONS ; < host _ name > ; < service _ description >
: param service : service to edit
: type service : alignak . objects . service . Service
... | if service . notifications_enabled :
service . modified_attributes |= DICT_MODATTR [ "MODATTR_NOTIFICATIONS_ENABLED" ] . value
service . notifications_enabled = False
self . send_an_element ( service . get_update_status_brok ( ) ) |
def _get_mean ( self , imt , mag , hypo_depth , rrup , d ) :
"""Return mean value as defined in equation 3.5.1-1 page 148""" | # clip magnitude at 8.3 as per note at page 3-36 in table Table 3.3.2-6
# in " Technical Reports on National Seismic Hazard Maps for Japan "
mag = min ( mag , 8.3 )
if imt . name == 'PGV' :
mean = ( 0.58 * mag + 0.0038 * hypo_depth + d - 1.29 - np . log10 ( rrup + 0.0028 * 10 ** ( 0.5 * mag ) ) - 0.002 * rrup )
els... |
def keys ( self ) :
"""Return a copy of the flat dictionary ' s list of keys .
See the note for : meth : ` flatdict . FlatDict . items ` .
: rtype : list""" | keys = [ ]
for key , value in self . _values . items ( ) :
if isinstance ( value , ( FlatDict , dict ) ) :
nested = [ self . _delimiter . join ( [ key , k ] ) for k in value . keys ( ) ]
keys += nested if nested else [ key ]
else :
keys . append ( key )
return sorted ( keys ) |
def buildNavigation ( self ) :
"""Chooses the appropriate layout navigation component based on user prefs""" | if self . buildSpec [ 'navigation' ] == constants . TABBED :
navigation = Tabbar ( self , self . buildSpec , self . configs )
else :
navigation = Sidebar ( self , self . buildSpec , self . configs )
if self . buildSpec [ 'navigation' ] == constants . HIDDEN :
navigation . Hide ( )
return navigation |
def _process ( self , data_buffer ) :
"""Handle incoming packet from server .""" | packet = json . loads ( data_buffer )
if packet [ 'cmd' ] == 'out' : # Call os . write manually . In Python2.6 , sys . stdout . write doesn ' t use UTF - 8.
original_mode = DWORD ( 0 )
windll . kernel32 . GetConsoleMode ( self . _hconsole , byref ( original_mode ) )
windll . kernel32 . SetConsoleMode ( self... |
def initialize_fields ( self , content ) :
"""Initializes the : class : ` Field ` elements in the ` Array ` with the
* values * in the * content * list .
If the * content * list is shorter than the ` Array ` then the * content *
list is used as a rotating fill pattern for the : class : ` Field ` elements
in... | if isinstance ( content , ( list , tuple ) ) :
capacity = len ( content )
for i in range ( 0 , len ( self ) , capacity ) :
for name , pair in enumerate ( zip ( self [ i : i + capacity ] , content ) , start = i ) :
item , value = pair
if is_mixin ( item ) : # Container or Pointer
... |
def _prepare_load_balancers ( self ) :
"""Prepare load balancer variables""" | stack = { A . NAME : self [ A . NAME ] , A . VERSION : self [ A . VERSION ] , }
for load_balancer in self . get ( R . LOAD_BALANCERS , [ ] ) :
svars = { A . STACK : stack }
load_balancer [ A . loadbalancer . VARS ] = svars |
def get_top_edge_depth ( self ) :
"""Return minimum depth of surface ' s top edge .
: returns :
Float value , the vertical distance between the earth surface
and the shallowest point in surface ' s top edge in km .""" | top_edge = self . mesh [ 0 : 1 ]
if top_edge . depths is None :
return 0
else :
return numpy . min ( top_edge . depths ) |
def extractFieldsFromResult ( data ) :
'''Method that parses Infobel textual information to return a series of attributes .
: return : a list of i3visio - like objects .''' | entities = [ ]
# Defining the objects to extract
fieldsRegExp = { }
fieldsRegExp [ "i3visio.fullname" ] = "<span class=\"fn\">([^<]*)</span>"
fieldsRegExp [ "i3visio.name" ] = " por <strong>[^ ]* ([^<]*)</strong>"
fieldsRegExp [ "i3visio.surname" ] = " por <strong>([^ ]*) "
fieldsRegExp [ "i3visio.location.addres... |
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