idx int64 0 252k | question stringlengths 48 5.28k | target stringlengths 5 1.23k |
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8,400 | def gen_schlumberger ( self , M , N , a = None ) : if a is None : a = np . abs ( M - N ) nr_of_steps_left = int ( min ( M , N ) - 1 / a ) nr_of_steps_right = int ( ( self . nr_electrodes - max ( M , N ) ) / a ) configs = [ ] for i in range ( 0 , min ( nr_of_steps_left , nr_of_steps_right ) ) : A = min ( M , N ) - ( i +... | generate one Schlumberger sounding configuration that is one set of configurations for one potential dipole MN . |
8,401 | def add_to_configs ( self , configs ) : if len ( configs ) == 0 : return None if self . configs is None : self . configs = np . atleast_2d ( configs ) else : configs = np . atleast_2d ( configs ) self . configs = np . vstack ( ( self . configs , configs ) ) return self . configs | Add one or more measurement configurations to the stored configurations |
8,402 | def split_into_normal_and_reciprocal ( self , pad = False , return_indices = False ) : configs = np . hstack ( ( np . sort ( self . configs [ : , 0 : 2 ] , axis = 1 ) , np . sort ( self . configs [ : , 2 : 4 ] , axis = 1 ) ) ) ab_min = configs [ : , 0 ] mn_min = configs [ : , 2 ] indices_normal = np . where ( ab_min < ... | Split the stored configurations into normal and reciprocal measurements |
8,403 | def gen_reciprocals ( self , append = False ) : reciprocals = self . configs . copy ( ) [ : , : : - 1 ] reciprocals [ : , 0 : 2 ] = np . sort ( reciprocals [ : , 0 : 2 ] , axis = 1 ) reciprocals [ : , 2 : 4 ] = np . sort ( reciprocals [ : , 2 : 4 ] , axis = 1 ) ind = np . lexsort ( ( reciprocals [ : , 3 ] , reciprocals... | Generate reciprocal configurations sort by AB and optionally append to configurations . |
8,404 | def gen_configs_permutate ( self , injections_raw , only_same_dipole_length = False , ignore_crossed_dipoles = False , silent = False ) : injections = np . atleast_2d ( injections_raw ) . astype ( int ) N = injections . shape [ 0 ] measurements = [ ] for injection in range ( 0 , N ) : dipole_length = np . abs ( injecti... | Create measurement configurations out of a pool of current injections . Use only the provided dipoles for potential dipole selection . This means that we have always reciprocal measurements . |
8,405 | def remove_max_dipole_sep ( self , maxsep = 10 ) : sep = np . abs ( self . configs [ : , 1 ] - self . configs [ : , 2 ] ) self . configs = self . configs [ sep <= maxsep ] | Remove configurations with dipole separations higher than maxsep . |
8,406 | def to_pg_scheme ( self , container = None , positions = None ) : if container is None and positions is None : raise Exception ( 'electrode positions are required for BERT export' ) if container is not None and container . electrodes is None : raise Exception ( 'container does not contain electrode positions' ) if cont... | Convert the configuration to a pygimli measurement scheme |
8,407 | def to_iris_syscal ( self , filename ) : with open ( filename , 'w' ) as fid : fid . write ( '#\t X\t Y\t Z\n' ) for nr in range ( 0 , self . configs . max ( ) ) : fid . write ( '{} {} 0 0\n' . format ( nr + 1 , nr ) ) fid . write ( '#\t A\t B\t M\t N\n' ) for nr , config in enumerate ( self . configs ) : fid . wr... | Export to IRIS Instrument configuration file |
8,408 | def create_plan ( self , * , plan_code , description , interval , interval_count , max_payments_allowed , payment_attempts_delay , plan_value , plan_tax , plan_tax_return_base , currency , max_payment_attempts = None , max_pending_payments = None , trial_days = None ) : payload = { "accountId" : self . client . account... | Creating a new plan for subscriptions associated with the merchant . |
8,409 | def get_plan ( self , plan_code ) : return self . client . _get ( self . url + 'plans/{}' . format ( plan_code ) , headers = self . get_headers ( ) ) | Check all the information of a plan for subscriptions associated with the merchant . |
8,410 | def delete_plan ( self , plan_code ) : return self . client . _delete ( self . url + 'plans/{}' . format ( plan_code ) , headers = self . get_headers ( ) ) | Delete an entire subscription plan associated with the merchant . |
8,411 | def create_customer ( self , * , full_name , email ) : payload = { "fullName" : full_name , "email" : email } return self . client . _post ( self . url + 'customers' , json = payload , headers = self . get_headers ( ) ) | Creation of a customer in the system . |
8,412 | def get_customer ( self , customer_id ) : return self . client . _get ( self . url + 'customers/{}' . format ( customer_id ) , headers = self . get_headers ( ) ) | Queries the information related to the customer . |
8,413 | def delete_customer ( self , customer_id ) : return self . client . _delete ( self . url + 'customers/{}' . format ( customer_id ) , headers = self . get_headers ( ) ) | Removes a user from the system . |
8,414 | def create_subscription ( self , * , customer_id , credit_card_token , plan_code , quantity = None , installments = None , trial_days = None , immediate_payment = None , extra1 = None , extra2 = None , delivery_address = None , notify_url = None , recurring_bill_items = None ) : payload = { "quantity" : quantity , "ins... | Creating a new subscription of a client to a plan . |
8,415 | def get_subscription ( self , subscription_id ) : return self . client . _put ( self . url + 'subscriptions/{}' . format ( subscription_id ) , headers = self . get_headers ( ) ) | Check the basic information associated with the specified subscription . |
8,416 | def update_subscription ( self , * , subscription_id , credit_card_token ) : payload = { "creditCardToken" : credit_card_token } fmt = 'subscriptions/{}' . format ( subscription_id ) return self . client . _put ( self . url + fmt , json = payload , headers = self . get_headers ( ) ) | Update information associated with the specified subscription . At the moment it is only possible to update the token of the credit card to which the charge of the subscription is made . |
8,417 | def delete_subscription ( self , subscription_id ) : return self . client . _delete ( self . url + 'subscriptions/{}' . format ( subscription_id ) , headers = self . get_headers ( ) ) | Unsubscribe delete the relationship of the customer with the plan . |
8,418 | def create_additional_charge ( self , * , subscription_id , description , plan_value , plan_tax , plan_tax_return_base , currency ) : payload = { "description" : description , "additionalValues" : [ { "name" : "ITEM_VALUE" , "value" : plan_value , "currency" : currency } , { "name" : "ITEM_TAX" , "value" : plan_tax , "... | Adds extra charges to the respective invoice for the current period . |
8,419 | def get_additional_charge_by_identifier ( self , recurring_billing_id ) : fmt = 'recurringBillItems/{}' . format ( recurring_billing_id ) return self . client . _get ( self . url + fmt , headers = self . get_headers ( ) ) | Query extra charge information of an invoice from its identifier . |
8,420 | def update_additional_charge ( self , * , recurring_billing_id , description , plan_value , plan_tax , plan_tax_return_base , currency ) : payload = { "description" : description , "additionalValues" : [ { "name" : "ITEM_VALUE" , "value" : plan_value , "currency" : currency } , { "name" : "ITEM_TAX" , "value" : plan_ta... | Updates the information from an additional charge in an invoice . |
8,421 | def delete_additional_charge ( self , recurring_billing_id ) : fmt = 'recurringBillItems/{}' . format ( recurring_billing_id ) return self . client . _delete ( self . url + fmt , headers = self . get_headers ( ) ) | Remove an extra charge from an invoice . |
8,422 | def thumbnail ( parser , token ) : args = token . split_contents ( ) tag = args [ 0 ] if len ( args ) > 4 and args [ - 2 ] == 'as' : context_name = args [ - 1 ] args = args [ : - 2 ] else : context_name = None if len ( args ) < 3 : raise TemplateSyntaxError ( "Invalid syntax. Expected " "'{%% %s source size [option1 op... | Creates a thumbnail of for an ImageField . |
8,423 | def printStats ( self ) : print ( "--- Imagestats Results ---" ) if ( self . fields . find ( 'npix' ) != - 1 ) : print ( "Number of pixels : " , self . npix ) if ( self . fields . find ( 'min' ) != - 1 ) : print ( "Minimum value : " , self . min ) if ( self . fields . find ( 'max' ) != - 1 ) : print ( "Maximum v... | Print the requested statistics values for those fields specified on input . |
8,424 | def raw_request ( self , method , uri , ** kwargs ) : with warnings . catch_warnings ( ) : warnings . simplefilter ( "ignore" , urllib3 . exceptions . InsecureRequestWarning ) warnings . simplefilter ( "ignore" , urllib3 . exceptions . InsecurePlatformWarning ) try : response = self . _get_session ( ) . request ( metho... | Perform a WVA web services request and return the raw response object |
8,425 | def request ( self , method , uri , ** kwargs ) : response = self . raw_request ( method , uri , ** kwargs ) if response . status_code != 200 : exception_class = HTTP_STATUS_EXCEPTION_MAP . get ( response . status_code , WVAHttpError ) raise exception_class ( response ) if response . headers . get ( "content-type" ) ==... | Perform a WVA web services request and return the decoded value if successful |
8,426 | def post ( self , uri , data , ** kwargs ) : return self . request ( "POST" , uri , data = data , ** kwargs ) | POST the provided data to the specified path |
8,427 | def post_json ( self , uri , data , ** kwargs ) : encoded_data = json . dumps ( data ) kwargs . setdefault ( "headers" , { } ) . update ( { "Content-Type" : "application/json" , } ) return self . post ( uri , data = encoded_data , ** kwargs ) | POST the provided data as json to the specified path |
8,428 | def put ( self , uri , data , ** kwargs ) : return self . request ( "PUT" , uri , data = data , ** kwargs ) | PUT the provided data to the specified path |
8,429 | def put_json ( self , uri , data , ** kwargs ) : encoded_data = json . dumps ( data ) kwargs . setdefault ( "headers" , { } ) . update ( { "Content-Type" : "application/json" , } ) return self . put ( uri , data = encoded_data , ** kwargs ) | PUT the provided data as json to the specified path |
8,430 | def mac_to_ipv6_linklocal ( mac , prefix = "fe80::" ) : mac_value = int ( mac . translate ( str . maketrans ( dict ( [ ( x , None ) for x in [ " " , "." , ":" , "-" ] ] ) ) ) , 16 ) high2 = mac_value >> 32 & 0xffff ^ 0x0200 high1 = mac_value >> 24 & 0xff low1 = mac_value >> 16 & 0xff low2 = mac_value & 0xffff return pr... | Translate a MAC address into an IPv6 address in the prefixed network . |
8,431 | def datagram_received ( self , data , addr ) : self . register ( ) response = unpack_lifx_message ( data ) self . lastmsg = datetime . datetime . now ( ) if response . seq_num in self . message : response_type , myevent , callb = self . message [ response . seq_num ] if type ( response ) == response_type : if response ... | Method run when data is received from the device |
8,432 | def register ( self ) : if not self . registered : self . registered = True if self . parent : self . parent . register ( self ) | Proxy method to register the device with the parent . |
8,433 | def unregister ( self ) : if self . registered : if datetime . datetime . now ( ) - datetime . timedelta ( seconds = self . unregister_timeout ) > self . lastmsg : self . registered = False if self . parent : self . parent . unregister ( self ) | Proxy method to unregister the device with the parent . |
8,434 | async def fire_sending ( self , msg , num_repeats ) : if num_repeats is None : num_repeats = self . retry_count sent_msg_count = 0 sleep_interval = 0.05 while ( sent_msg_count < num_repeats ) : if self . transport : self . transport . sendto ( msg . packed_message ) sent_msg_count += 1 await aio . sleep ( sleep_interva... | Coroutine used to send message to the device when no response is needed . |
8,435 | async def try_sending ( self , msg , timeout_secs , max_attempts ) : if timeout_secs is None : timeout_secs = self . timeout if max_attempts is None : max_attempts = self . retry_count attempts = 0 while attempts < max_attempts : if msg . seq_num not in self . message : return event = aio . Event ( ) self . message [ m... | Coroutine used to send message to the device when a response or ack is needed . |
8,436 | def req_with_ack ( self , msg_type , payload , callb = None , timeout_secs = None , max_attempts = None ) : msg = msg_type ( self . mac_addr , self . source_id , seq_num = self . seq_next ( ) , payload = payload , ack_requested = True , response_requested = False ) self . message [ msg . seq_num ] = [ Acknowledgement ,... | Method to send a message expecting to receive an ACK . |
8,437 | def get_label ( self , callb = None ) : if self . label is None : mypartial = partial ( self . resp_set_label ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) response = self . req_with_resp ( GetLabel , StateLabel , callb = mycallb ) return sel... | Convenience method to request the label from the device |
8,438 | def set_label ( self , value , callb = None ) : if len ( value ) > 32 : value = value [ : 32 ] mypartial = partial ( self . resp_set_label , label = value ) if callb : self . req_with_ack ( SetLabel , { "label" : value } , lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) ) else : self . req_with_ack ( SetLabel , { ... | Convenience method to set the label of the device |
8,439 | def get_location ( self , callb = None ) : if self . location is None : mypartial = partial ( self . resp_set_location ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) response = self . req_with_resp ( GetLocation , StateLocation , callb = mycal... | Convenience method to request the location from the device |
8,440 | def get_group ( self , callb = None ) : if self . group is None : mypartial = partial ( self . resp_set_group ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) response = self . req_with_resp ( GetGroup , StateGroup , callb = callb ) return self ... | Convenience method to request the group from the device |
8,441 | def get_wififirmware ( self , callb = None ) : if self . wifi_firmware_version is None : mypartial = partial ( self . resp_set_wififirmware ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) response = self . req_with_resp ( GetWifiFirmware , Stat... | Convenience method to request the wifi firmware info from the device |
8,442 | def resp_set_wififirmware ( self , resp ) : if resp : self . wifi_firmware_version = float ( str ( str ( resp . version >> 16 ) + "." + str ( resp . version & 0xff ) ) ) self . wifi_firmware_build_timestamp = resp . build | Default callback for get_wififirmware |
8,443 | def get_wifiinfo ( self , callb = None ) : response = self . req_with_resp ( GetWifiInfo , StateWifiInfo , callb = callb ) return None | Convenience method to request the wifi info from the device |
8,444 | def get_hostfirmware ( self , callb = None ) : if self . host_firmware_version is None : mypartial = partial ( self . resp_set_hostfirmware ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) response = self . req_with_resp ( GetHostFirmware , Stat... | Convenience method to request the device firmware info from the device |
8,445 | def resp_set_hostfirmware ( self , resp ) : if resp : self . host_firmware_version = float ( str ( str ( resp . version >> 16 ) + "." + str ( resp . version & 0xff ) ) ) self . host_firmware_build_timestamp = resp . build | Default callback for get_hostfirmware |
8,446 | def get_hostinfo ( self , callb = None ) : response = self . req_with_resp ( GetInfo , StateInfo , callb = callb ) return None | Convenience method to request the device info from the device |
8,447 | def get_version ( self , callb = None ) : if self . vendor is None : mypartial = partial ( self . resp_set_version ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) response = self . req_with_resp ( GetVersion , StateVersion , callb = mycallb ) r... | Convenience method to request the version from the device |
8,448 | def resp_set_version ( self , resp ) : if resp : self . vendor = resp . vendor self . product = resp . product self . version = resp . version | Default callback for get_version |
8,449 | def resp_set_lightpower ( self , resp , power_level = None ) : if power_level is not None : self . power_level = power_level elif resp : self . power_level = resp . power_level | Default callback for set_power |
8,450 | def get_color ( self , callb = None ) : response = self . req_with_resp ( LightGet , LightState , callb = callb ) return self . color | Convenience method to request the colour status from the device |
8,451 | def set_color ( self , value , callb = None , duration = 0 , rapid = False ) : if len ( value ) == 4 : mypartial = partial ( self . resp_set_light , color = value ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) if rapid : self . fire_and_forget... | Convenience method to set the colour status of the device |
8,452 | def resp_set_light ( self , resp , color = None ) : if color : self . color = color elif resp : self . power_level = resp . power_level self . color = resp . color self . label = resp . label . decode ( ) . replace ( "\x00" , "" ) | Default callback for set_color |
8,453 | def get_color_zones ( self , start_index , end_index = None , callb = None ) : if end_index is None : end_index = start_index + 7 args = { "start_index" : start_index , "end_index" : end_index , } self . req_with_resp ( MultiZoneGetColorZones , MultiZoneStateMultiZone , payload = args , callb = callb ) | Convenience method to request the state of colour by zones from the device |
8,454 | def set_color_zones ( self , start_index , end_index , color , duration = 0 , apply = 1 , callb = None , rapid = False ) : if len ( color ) == 4 : args = { "start_index" : start_index , "end_index" : end_index , "color" : color , "duration" : duration , "apply" : apply , } mypartial = partial ( self . resp_set_multizon... | Convenience method to set the colour status zone of the device |
8,455 | def get_infrared ( self , callb = None ) : response = self . req_with_resp ( LightGetInfrared , LightStateInfrared , callb = callb ) return self . infrared_brightness | Convenience method to request the infrared brightness from the device |
8,456 | def set_infrared ( self , infrared_brightness , callb = None , rapid = False ) : mypartial = partial ( self . resp_set_infrared , infrared_brightness = infrared_brightness ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) if rapid : self . fire_a... | Convenience method to set the infrared status of the device |
8,457 | def start ( self , listen_ip = LISTEN_IP , listen_port = 0 ) : coro = self . loop . create_datagram_endpoint ( lambda : self , local_addr = ( listen_ip , listen_port ) ) self . task = self . loop . create_task ( coro ) return self . task | Start discovery task . |
8,458 | def connection_made ( self , transport ) : self . transport = transport sock = self . transport . get_extra_info ( "socket" ) sock . setsockopt ( socket . SOL_SOCKET , socket . SO_REUSEADDR , 1 ) sock . setsockopt ( socket . SOL_SOCKET , socket . SO_BROADCAST , 1 ) self . loop . call_soon ( self . discover ) | Method run when the UDP broadcast server is started |
8,459 | def datagram_received ( self , data , addr ) : response = unpack_lifx_message ( data ) response . ip_addr = addr [ 0 ] mac_addr = response . target_addr if mac_addr == BROADCAST_MAC : return if type ( response ) == StateService and response . service == 1 : remote_port = response . port elif type ( response ) == LightS... | Method run when data is received from the devices |
8,460 | def discover ( self ) : if self . transport : if self . discovery_countdown <= 0 : self . discovery_countdown = self . discovery_interval msg = GetService ( BROADCAST_MAC , self . source_id , seq_num = 0 , payload = { } , ack_requested = False , response_requested = True ) self . transport . sendto ( msg . generate_pac... | Method to send a discovery message |
8,461 | async def scan ( self , timeout = 1 ) : adapters = await self . loop . run_in_executor ( None , ifaddr . get_adapters ) ips = [ ip . ip for adapter in ifaddr . get_adapters ( ) for ip in adapter . ips if ip . is_IPv4 ] if not ips : return [ ] tasks = [ ] discoveries = [ ] for ip in ips : manager = ScanManager ( ip ) li... | Return a list of local IP addresses on interfaces with LIFX bulbs . |
8,462 | def _get_file_version ( filename ) : mat = sio . loadmat ( filename , squeeze_me = True ) version = mat [ 'MP' ] [ 'Version' ] . item ( ) del ( mat ) return version | High level import function that tries to determine the specific version of the data format used . |
8,463 | def MD_ConfigsPermutate ( df_md ) : g_current_injections = df_md . groupby ( [ 'a' , 'b' ] ) ab = np . array ( list ( g_current_injections . groups . keys ( ) ) ) config_mgr = ConfigManager ( nr_of_electrodes = ab . max ( ) ) config_mgr . gen_configs_permutate ( ab , silent = True ) return config_mgr . configs | Given a MD DataFrame return a Nx4 array which permutes the current injection dipoles . |
8,464 | def apply_correction_factors ( df , correction_file ) : if isinstance ( correction_file , ( list , tuple ) ) : corr_data_raw = np . vstack ( [ np . loadtxt ( x ) for x in correction_file ] ) else : corr_data_raw = np . loadtxt ( correction_file ) if corr_data_raw . shape [ 1 ] == 3 : A = ( corr_data_raw [ : , 0 ] / 1e4... | Apply correction factors for a pseudo - 2D measurement setup . See Weigand and Kemna 2017 Biogeosciences for detailed information . |
8,465 | def get_pij_method ( model = F81 , frequencies = None , kappa = None ) : if is_f81_like ( model ) : mu = get_mu ( frequencies ) return lambda t : get_f81_pij ( t , frequencies , mu ) if JTT == model : return get_jtt_pij if HKY == model : return lambda t : get_hky_pij ( t , frequencies , kappa ) | Returns a function for calculation of probability matrix of substitutions i - > j over time t . |
8,466 | def initialize_allowed_states ( tree , feature , states ) : allowed_states_feature = get_personalized_feature_name ( feature , ALLOWED_STATES ) state2index = dict ( zip ( states , range ( len ( states ) ) ) ) for node in tree . traverse ( ) : node_states = getattr ( node , feature , set ( ) ) if not node_states : allow... | Initializes the allowed state arrays for tips based on their states given by the feature . |
8,467 | def alter_zero_tip_allowed_states ( tree , feature ) : zero_parent2tips = defaultdict ( list ) allowed_state_feature = get_personalized_feature_name ( feature , ALLOWED_STATES ) for tip in tree : if tip . dist == 0 : state = getattr ( tip , feature , None ) if state is not None and state != '' : zero_parent2tips [ tip ... | Alters the bottom - up likelihood arrays for zero - distance tips to make sure they do not contradict with other zero - distance tip siblings . |
8,468 | def unalter_zero_tip_allowed_states ( tree , feature , state2index ) : allowed_state_feature = get_personalized_feature_name ( feature , ALLOWED_STATES ) for tip in tree : if tip . dist > 0 : continue state = getattr ( tip , feature , set ( ) ) if state : initial_allowed_states = np . zeros ( len ( state2index ) , np .... | Unalters the bottom - up likelihood arrays for zero - distance tips to contain ones only in their states . |
8,469 | def unalter_zero_tip_joint_states ( tree , feature , state2index ) : lh_joint_state_feature = get_personalized_feature_name ( feature , BU_LH_JOINT_STATES ) for tip in tree : if tip . dist > 0 : continue state = getattr ( tip , feature , set ( ) ) if len ( state ) > 1 : allowed_indices = { state2index [ _ ] for _ in st... | Unalters the joint tip states for zero - distance tips to contain only their states . |
8,470 | def calculate_marginal_likelihoods ( tree , feature , frequencies ) : bu_lh_feature = get_personalized_feature_name ( feature , BU_LH ) bu_lh_sf_feature = get_personalized_feature_name ( feature , BU_LH_SF ) td_lh_feature = get_personalized_feature_name ( feature , TD_LH ) td_lh_sf_feature = get_personalized_feature_na... | Calculates marginal likelihoods for each tree node by multiplying state frequencies with their bottom - up and top - down likelihoods . |
8,471 | def convert_likelihoods_to_probabilities ( tree , feature , states ) : lh_feature = get_personalized_feature_name ( feature , LH ) name2probs = { } for node in tree . traverse ( ) : lh = getattr ( node , lh_feature ) name2probs [ node . name ] = lh / lh . sum ( ) return pd . DataFrame . from_dict ( name2probs , orient ... | Normalizes each node marginal likelihoods to convert them to marginal probabilities . |
8,472 | def choose_ancestral_states_mppa ( tree , feature , states , force_joint = True ) : lh_feature = get_personalized_feature_name ( feature , LH ) allowed_state_feature = get_personalized_feature_name ( feature , ALLOWED_STATES ) joint_state_feature = get_personalized_feature_name ( feature , JOINT_STATE ) n = len ( state... | Chooses node ancestral states based on their marginal probabilities using MPPA method . |
8,473 | def choose_ancestral_states_map ( tree , feature , states ) : lh_feature = get_personalized_feature_name ( feature , LH ) allowed_state_feature = get_personalized_feature_name ( feature , ALLOWED_STATES ) _ , state2array = get_state2allowed_states ( states , False ) for node in tree . traverse ( ) : marginal_likelihood... | Chooses node ancestral states based on their marginal probabilities using MAP method . |
8,474 | def choose_ancestral_states_joint ( tree , feature , states , frequencies ) : lh_feature = get_personalized_feature_name ( feature , BU_LH ) lh_state_feature = get_personalized_feature_name ( feature , BU_LH_JOINT_STATES ) allowed_state_feature = get_personalized_feature_name ( feature , ALLOWED_STATES ) joint_state_fe... | Chooses node ancestral states based on their marginal probabilities using joint method . |
8,475 | def col_name2cat ( column ) : column_string = '' . join ( s for s in column . replace ( ' ' , '_' ) if s . isalnum ( ) or '_' == s ) return column_string | Reformats the column string to make sure it contains only numerical letter characters or underscore . |
8,476 | def get_user_config_filename ( appname = 'notify' ) : import platform system = platform . system ( ) if system == 'Windows' : rootname = os . path . join ( os . environ [ 'APPDATA' ] , appname ) filename = appname + ".cfg" prefix = '' elif system == 'Linux' : XDG_CONFIG_HOME = os . environ . get ( 'XDG_CONFIG_HOME' , N... | Get user config filename . |
8,477 | def config_to_options ( config ) : class Options : host = config . get ( 'smtp' , 'host' , raw = True ) port = config . getint ( 'smtp' , 'port' ) to_addr = config . get ( 'mail' , 'to_addr' , raw = True ) from_addr = config . get ( 'mail' , 'from_addr' , raw = True ) subject = config . get ( 'mail' , 'subject' , raw =... | Convert ConfigParser instance to argparse . Namespace |
8,478 | def create_default_config ( ) : import codecs config = ConfigParser . SafeConfigParser ( ) config . readfp ( StringIO ( DEFAULT_CONFIG ) ) filename = get_user_config_filename ( ) if not os . path . exists ( filename ) : from wizard import setup_wizard setup_wizard ( config ) else : try : fi = codecs . open ( filename ,... | Create default ConfigParser instance |
8,479 | def has_multiple_timesteps ( data ) : if "timestep" in data . keys ( ) : if len ( np . unique ( data [ "timestep" ] ) ) > 1 : return True return False | Return True if data container has multiple timesteps . |
8,480 | def split_timesteps ( data , consistent_abmn = False ) : if has_multiple_timesteps ( data ) : grouped = data . groupby ( "timestep" ) return [ group [ 1 ] for group in grouped ] else : return data | Split data into multiple timesteps . |
8,481 | def parse ( text ) : fixed_text = validate . fix_string_case ( utf ( text ) ) output = [ ] cur_end = 0 for cur , i in enumerate ( fixed_text ) : try : i . encode ( 'utf-8' ) except UnicodeDecodeError : uni_pass = False else : uni_pass = True match = { 'matched' : False } if not uni_pass : cur_end = cur + 1 output . app... | Parses input text matches and replaces using avrodict |
8,482 | def match_non_rule_patterns ( fixed_text , cur = 0 ) : pattern = exact_find_in_pattern ( fixed_text , cur , NON_RULE_PATTERNS ) if len ( pattern ) > 0 : return { "matched" : True , "found" : pattern [ 0 ] [ 'find' ] , "replaced" : pattern [ 0 ] [ 'replace' ] } else : return { "matched" : False , "found" : None , "repla... | Matches given text at cursor position with non rule patterns |
8,483 | def match_rule_patterns ( fixed_text , cur = 0 ) : pattern = exact_find_in_pattern ( fixed_text , cur , RULE_PATTERNS ) if len ( pattern ) > 0 : return { "matched" : True , "found" : pattern [ 0 ] [ 'find' ] , "replaced" : pattern [ 0 ] [ 'replace' ] , "rules" : pattern [ 0 ] [ 'rules' ] } else : return { "matched" : F... | Matches given text at cursor position with rule patterns |
8,484 | def exact_find_in_pattern ( fixed_text , cur = 0 , patterns = PATTERNS ) : return [ x for x in patterns if ( cur + len ( x [ 'find' ] ) <= len ( fixed_text ) ) and x [ 'find' ] == fixed_text [ cur : ( cur + len ( x [ 'find' ] ) ) ] ] | Returns pattern items that match given text cur position and pattern |
8,485 | def process_rules ( rules , fixed_text , cur = 0 , cur_end = 1 ) : replaced = '' for rule in rules : matched = False for match in rule [ 'matches' ] : matched = process_match ( match , fixed_text , cur , cur_end ) if not matched : break if matched : replaced = rule [ 'replace' ] break if matched : return replaced else ... | Process rules matched in pattern and returns suitable replacement |
8,486 | def process_match ( match , fixed_text , cur , cur_end ) : replace = True if match [ 'type' ] == 'prefix' : chk = cur - 1 else : chk = cur_end if match [ 'scope' ] . startswith ( '!' ) : scope = match [ 'scope' ] [ 1 : ] negative = True else : scope = match [ 'scope' ] negative = False if scope == 'punctuation' : if ( ... | Processes a single match in rules |
8,487 | def cli ( ctx , hostname , username , password , config_dir , https ) : ctx . is_root = True ctx . user_values_entered = False ctx . config_dir = os . path . abspath ( os . path . expanduser ( config_dir ) ) ctx . config = load_config ( ctx ) ctx . hostname = hostname ctx . username = username ctx . password = password... | Command - line interface for interacting with a WVA device |
8,488 | def get ( ctx , uri ) : http_client = get_wva ( ctx ) . get_http_client ( ) cli_pprint ( http_client . get ( uri ) ) | Perform an HTTP GET of the provided URI |
8,489 | def delete ( ctx , uri ) : http_client = get_wva ( ctx ) . get_http_client ( ) cli_pprint ( http_client . delete ( uri ) ) | DELETE the specified URI |
8,490 | def post ( ctx , uri , input_file ) : http_client = get_wva ( ctx ) . get_http_client ( ) cli_pprint ( http_client . post ( uri , input_file . read ( ) ) ) | POST file data to a specific URI |
8,491 | def sample ( ctx , element , timestamp , repeat , delay ) : element = get_wva ( ctx ) . get_vehicle_data_element ( element ) for i in xrange ( repeat ) : curval = element . sample ( ) if timestamp : print ( "{} at {}" . format ( curval . value , curval . timestamp . ctime ( ) ) ) else : print ( "{}" . format ( curval .... | Sample the value of a vehicle data element |
8,492 | def list ( ctx ) : wva = get_wva ( ctx ) for subscription in wva . get_subscriptions ( ) : print ( subscription . short_name ) | List short name of all current subscriptions |
8,493 | def delete ( ctx , short_name ) : wva = get_wva ( ctx ) subscription = wva . get_subscription ( short_name ) subscription . delete ( ) | Delete a specific subscription by short name |
8,494 | def clear ( ctx ) : wva = get_wva ( ctx ) for subscription in wva . get_subscriptions ( ) : sys . stdout . write ( "Deleting {}... " . format ( subscription . short_name ) ) sys . stdout . flush ( ) subscription . delete ( ) print ( "Done" ) | Remove all registered subscriptions |
8,495 | def show ( ctx , short_name ) : wva = get_wva ( ctx ) subscription = wva . get_subscription ( short_name ) cli_pprint ( subscription . get_metadata ( ) ) | Show metadata for a specific subscription |
8,496 | def add ( ctx , short_name , uri , interval , buffer ) : wva = get_wva ( ctx ) subscription = wva . get_subscription ( short_name ) subscription . create ( uri , buffer , interval ) | Add a subscription with a given short_name for a given uri |
8,497 | def listen ( ctx ) : wva = get_wva ( ctx ) es = wva . get_event_stream ( ) def cb ( event ) : cli_pprint ( event ) es . add_event_listener ( cb ) es . enable ( ) while True : time . sleep ( 5 ) | Output the contents of the WVA event stream |
8,498 | def graph ( ctx , items , seconds , ylim ) : wva = get_wva ( ctx ) es = wva . get_event_stream ( ) try : from wva import grapher except ImportError : print ( "Unable to graph... you must have matplotlib installed" ) else : stream_grapher = grapher . WVAStreamGrapher ( wva , items , seconds = seconds , ylim = ylim ) es ... | Present a live graph of the incoming streaming data |
8,499 | def authorize ( ctx , public_key , append ) : wva = get_wva ( ctx ) http_client = wva . get_http_client ( ) authorized_keys_uri = "/files/userfs/WEB/python/.ssh/authorized_keys" authorized_key_contents = public_key if append : try : existing_contents = http_client . get ( authorized_keys_uri ) authorized_key_contents =... | Enable ssh login as the Python user for the current user |
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