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def update ( self , ** kwargs ) : u for key , value in kwargs . items ( ) : helper = helpers . CAST_DICT . get ( type ( value ) , str ) tag = self . _get_aliases ( ) . get ( key , key ) elements = list ( self . _xml . iterchildren ( tag = tag ) ) if elements : for element in elements : element . text = helper ( value )...
u Updating or creation of new simple nodes .
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def sget ( self , path , default = NONE_NODE ) : u attrs = str ( path ) . split ( "." ) text_or_attr = None last_attr = attrs [ - 1 ] if last_attr == '#text' or last_attr . startswith ( '@' ) : text_or_attr = last_attr [ 1 : ] attrs = attrs [ : - 1 ] if default is NONE_NODE : default = None my_object = self for attr in...
u Enables access to nodes if one or more of them don t exist .
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def create ( self , tag , value ) : u child_tags = { child . tag for child in self . _xml } if tag in child_tags : raise KeyError ( 'Node {} already exists in XML tree.' . format ( tag ) ) self . set ( tag , value )
u Creates a node if it doesn t exist yet .
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def set ( self , name , value ) : u try : element = next ( self . _xml . iterchildren ( tag = name ) ) except StopIteration : element = etree . SubElement ( self . _xml , name ) if isinstance ( value , dict ) : self . assign_dict ( element , value ) elif isinstance ( value , ( list , tuple , set ) ) : self . assign_seq...
u Assigns a new XML structure to the node .
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def assign_dict ( self , node , xml_dict ) : new_node = etree . Element ( node . tag ) self . _xml . replace ( node , new_node ) helpers . dict_to_etree ( xml_dict , new_node )
Assigns a Python dict to a lxml node .
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def assign_literal ( element , value ) : u helper = helpers . CAST_DICT . get ( type ( value ) , str ) element . clear ( ) element . text = helper ( value )
u Assigns a literal .
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def to_dict ( self , ** kw ) : u _ , value = helpers . etree_to_dict ( self . _xml , ** kw ) . popitem ( ) return value
u Converts the lxml object to a dict .
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def _get_aliases ( self ) : u if self . _aliases is None : self . _aliases = { } if self . _xml is not None : for child in self . _xml . iterchildren ( ) : self . _aliases [ helpers . normalize_tag ( child . tag ) ] = child . tag return self . _aliases
u Creates a dict with aliases .
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def xpath ( self , path , namespaces = None , regexp = False , smart_strings = True , single_use = False , ) : u if ( namespaces in [ 'exslt' , 're' ] or ( regexp and not namespaces ) ) : namespaces = { 're' : "http://exslt.org/regular-expressions" } if single_use : node = self . _xml . xpath ( path ) else : xpe = self...
u Executes XPath query on the lxml object and returns a correct object .
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def xpath_evaluator ( self , namespaces = None , regexp = False , smart_strings = True ) : u return etree . XPathEvaluator ( self . _xml , namespaces = namespaces , regexp = regexp , smart_strings = smart_strings )
u Creates an XPathEvaluator instance for an ElementTree or an Element .
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def get_last_modified_date ( * args , ** kwargs ) : try : latest_note = Note . objects . latest ( ) latest_release = Release . objects . latest ( ) except ObjectDoesNotExist : return None return max ( latest_note . modified , latest_release . modified )
Returns the date of the last modified Note or Release .
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def using_ios_stash ( ) : print ( 'detected install path:' ) print ( os . path . dirname ( __file__ ) ) module_names = set ( sys . modules . keys ( ) ) return 'stash' in module_names or 'stash.system' in module_names
returns true if sys path hints the install is running on ios
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def get_partition_scores ( image , min_w = 1 , min_h = 1 ) : h , w = image . shape [ : 2 ] if w == 0 or h == 0 : return [ ] area = h * w cnz = numpy . count_nonzero total = cnz ( image ) if total == 0 or area == total : return [ ] if h < min_h * 2 : y_c = [ ] else : y_c = [ ( - abs ( ( count / ( ( h - y ) * w ) ) - ( (...
Return list of best to worst binary splits along the x and y axis .
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def __init_defaults ( self , config ) : provider = self . __provider if provider == 'sqlite' : config . setdefault ( 'dbname' , ':memory:' ) config . setdefault ( 'create_db' , True ) elif provider == 'mysql' : config . setdefault ( 'port' , 3306 ) config . setdefault ( 'charset' , 'utf8' ) elif provider == 'postgres' ...
Initializes the default connection settings .
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async def newnations ( self , root ) : return [ aionationstates . Nation ( n ) for n in root . find ( 'NEWNATIONS' ) . text . split ( ',' ) ]
Most recently founded nations from newest .
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async def regions ( self , root ) : return [ aionationstates . Region ( r ) for r in root . find ( 'REGIONS' ) . text . split ( ',' ) ]
List of all the regions seemingly in order of creation .
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def regionsbytag ( self , * tags ) : if len ( tags ) > 10 : raise ValueError ( 'You can specify up to 10 tags' ) if not tags : raise ValueError ( 'No tags specified' ) @ api_query ( 'regionsbytag' , tags = ',' . join ( tags ) ) async def result ( _ , root ) : text = root . find ( 'REGIONS' ) . text return ( [ aionation...
All regions with any of the named tags .
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def dispatch ( self , id ) : @ api_query ( 'dispatch' , dispatchid = str ( id ) ) async def result ( _ , root ) : elem = root . find ( 'DISPATCH' ) if not elem : raise NotFound ( f'No dispatch found with id {id}' ) return Dispatch ( elem ) return result ( self )
Dispatch by id .
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def dispatchlist ( self , * , author = None , category = None , subcategory = None , sort = 'new' ) : params = { 'sort' : sort } if author : params [ 'dispatchauthor' ] = author if category and subcategory : if ( category not in dispatch_categories or subcategory not in dispatch_categories [ category ] ) : raise ValueE...
Find dispatches by certain criteria .
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def poll ( self , id ) : @ api_query ( 'poll' , pollid = str ( id ) ) async def result ( _ , root ) : elem = root . find ( 'POLL' ) if not elem : raise NotFound ( f'No poll found with id {id}' ) return Poll ( elem ) return result ( self )
Poll with a given id .
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def banner ( self , * ids , _expand_macros = None ) : async def noop ( s ) : return s _expand_macros = _expand_macros or noop @ api_query ( 'banner' , banner = ',' . join ( ids ) ) async def result ( _ , root ) : banners = [ await Banner ( elem , _expand_macros ) for elem in root . find ( 'BANNERS' ) ] if not len ( ban...
Get data about banners by their ids .
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async def send_telegram ( self , * , client_key , telegram_id , telegram_key , recepient ) : params = { 'a' : 'sendTG' , 'client' : client_key , 'tgid' : str ( telegram_id ) , 'key' : telegram_key , 'to' : recepient } return await self . _call_api ( params )
A basic interface to the Telegrams API .
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async def happenings ( self , * , nations = None , regions = None , filters = None , beforeid = None , beforetime = None ) : while True : happening_bunch = await self . _get_happenings ( nations = nations , regions = regions , filters = filters , beforeid = beforeid , beforetime = beforetime ) for happening in happenin...
Iterate through happenings from newest to oldest .
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def find_potential_match_regions ( template , transformed_array , method = 'correlation' , raw_tolerance = 0.666 ) : if method == 'correlation' : match_value = np . sum ( template ** 2 ) elif method == 'squared difference' : match_value = 0 elif method == 'correlation coefficient' : temp_minus_mean = template - np . me...
To prevent prohibitively slow calculation of normalisation coefficient at each point in image find potential match points and normalise these only these . This function uses the definitions of the matching functions to calculate the expected match value and finds positions in the transformed array matching these - norm...
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def normalise_correlation ( image_tile_dict , transformed_array , template , normed_tolerance = 1 ) : template_norm = np . linalg . norm ( template ) image_norms = { ( x , y ) : np . linalg . norm ( image_tile_dict [ ( x , y ) ] ) * template_norm for ( x , y ) in image_tile_dict . keys ( ) } match_points = image_tile_d...
Calculates the normalisation coefficients of potential match positions Then normalises the correlation at these positions and returns them if they do indeed constitute a match
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def normalise_correlation_coefficient ( image_tile_dict , transformed_array , template , normed_tolerance = 1 ) : template_mean = np . mean ( template ) template_minus_mean = template - template_mean template_norm = np . linalg . norm ( template_minus_mean ) image_norms = { ( x , y ) : np . linalg . norm ( image_tile_d...
As above but for when the correlation coefficient matching method is used
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def calculate_squared_differences ( image_tile_dict , transformed_array , template , sq_diff_tolerance = 0.1 ) : template_norm_squared = np . sum ( template ** 2 ) image_norms_squared = { ( x , y ) : np . sum ( image_tile_dict [ ( x , y ) ] ** 2 ) for ( x , y ) in image_tile_dict . keys ( ) } match_points = image_tile_...
As above but for when the squared differences matching method is used
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async def post ( self ) : post = ( await self . region . _get_messages ( fromid = self . _post_id , limit = 1 ) ) [ 0 ] assert post . id == self . _post_id return post
Get the message lodged .
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async def resolution ( self ) : resolutions = await asyncio . gather ( aionationstates . ga . resolution_at_vote , aionationstates . sc . resolution_at_vote , ) for resolution in resolutions : if ( resolution is not None and resolution . name == self . resolution_name ) : return resolution raise aionationstates . NotFo...
Get the resolution voted on .
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async def proposal ( self ) : proposals = await aionationstates . wa . proposals ( ) for proposal in proposals : if ( proposal . name == self . proposal_name ) : return proposal raise aionationstates . NotFound
Get the proposal in question .
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def append ( self , electrode_id ) : do_append = False if not self . electrode_ids : do_append = True elif self . device . shape_indexes . shape [ 0 ] > 0 : source = self . electrode_ids [ - 1 ] target = electrode_id if not ( source == target ) : source_id , target_id = self . device . shape_indexes [ [ source , target...
Append the specified electrode to the route .
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def insert_surface ( self , position , name , surface , alpha = 1. ) : if name in self . df_surfaces . index : raise NameError ( 'Surface already exists with `name="{}"`.' . format ( name ) ) self . df_surfaces . loc [ name ] = surface , alpha surfaces_order = self . df_surfaces . index . values . tolist ( ) surfaces_o...
Insert Cairo surface as new layer .
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def append_surface ( self , name , surface , alpha = 1. ) : self . insert_surface ( position = self . df_surfaces . index . shape [ 0 ] , name = name , surface = surface , alpha = alpha )
Append Cairo surface as new layer on top of existing layers .
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def remove_surface ( self , name ) : self . df_surfaces . drop ( name , axis = 0 , inplace = True ) self . reorder_surfaces ( self . df_surfaces . index )
Remove layer from rendering stack and flatten remaining layers .
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def clone_surface ( self , source_name , target_name , target_position = - 1 , alpha = 1. ) : source_surface = self . df_surfaces . surface . ix [ source_name ] source_width = source_surface . get_width ( ) source_height = source_surface . get_height ( ) source_format = source_surface . get_format ( ) target_surface = ...
Clone surface from existing layer to a new name inserting new surface at specified position .
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def render_electrode_shapes ( self , df_shapes = None , shape_scale = 0.8 , fill = ( 1 , 1 , 1 ) ) : surface = self . get_surface ( ) if df_shapes is None : if hasattr ( self . canvas , 'df_canvas_shapes' ) : df_shapes = self . canvas . df_canvas_shapes else : return surface if 'x_center' not in df_shapes or 'y_center'...
Render electrode state shapes .
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def render_registration ( self ) : surface = self . get_surface ( ) if self . canvas is None or self . df_canvas_corners . shape [ 0 ] == 0 : return surface corners = self . df_canvas_corners . copy ( ) corners [ 'w' ] = 1 transform = self . canvas . shapes_to_canvas_transform canvas_corners = corners . values . dot ( ...
Render pinned points on video frame as red rectangle .
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def draw_route ( self , df_route , cr , color = None , line_width = None ) : df_route_centers = ( self . canvas . df_shape_centers . ix [ df_route . electrode_i ] [ [ 'x_center' , 'y_center' ] ] ) df_endpoint_marker = ( .6 * self . get_endpoint_marker ( df_route_centers ) + df_route_centers . iloc [ - 1 ] . values ) cr...
Draw a line between electrodes listed in a route .
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def on_widget__button_press_event ( self , widget , event ) : if self . mode == 'register_video' and event . button == 1 : self . start_event = event . copy ( ) return elif self . mode == 'control' : shape = self . canvas . find_shape ( event . x , event . y ) if shape is None : return state = event . get_state ( ) if ...
Called when any mouse button is pressed .
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def on_widget__button_release_event ( self , widget , event ) : event = event . copy ( ) if self . mode == 'register_video' and ( event . button == 1 and self . start_event is not None ) : self . emit ( 'point-pair-selected' , { 'start_event' : self . start_event , 'end_event' : event . copy ( ) } ) self . start_event ...
Called when any mouse button is released .
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def on_widget__motion_notify_event ( self , widget , event ) : if self . canvas is None : return elif event . is_hint : pointer = event . window . get_pointer ( ) x , y , mod_type = pointer else : x = event . x y = event . y shape = self . canvas . find_shape ( x , y ) self . widget . grab_focus ( ) if shape != self . ...
Called when mouse pointer is moved within drawing area .
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def register_electrode_command ( self , command , title = None , group = None ) : commands = self . electrode_commands . setdefault ( group , OrderedDict ( ) ) if title is None : title = ( command [ : 1 ] . upper ( ) + command [ 1 : ] ) . replace ( '_' , ' ' ) commands [ command ] = title
Register electrode command .
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def register_route_command ( self , command , title = None , group = None ) : commands = self . route_commands . setdefault ( group , OrderedDict ( ) ) if title is None : title = ( command [ : 1 ] . upper ( ) + command [ 1 : ] ) . replace ( '_' , ' ' ) commands [ command ] = title
Register route command .
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def after ( self ) : d = Deferred ( ) self . _after_deferreds . append ( d ) return d . chain
Return a deferred that will fire after the request is finished .
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def after_response ( self , request , fn , * args , ** kwargs ) : self . _requests [ id ( request ) ] [ "callbacks" ] . append ( ( fn , args , kwargs ) )
Call the given callable after the given request has its response .
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def plot_degbandshalffill ( ) : ulim = [ 3.45 , 5.15 , 6.85 , 8.55 ] bands = range ( 1 , 5 ) for band , u_int in zip ( bands , ulim ) : name = 'Z_half_' + str ( band ) + 'band' dop = [ 0.5 ] data = ssplt . calc_z ( band , dop , np . arange ( 0 , u_int , 0.1 ) , 0. , name ) plt . plot ( data [ 'u_int' ] , data [ 'zeta' ...
Plot of Quasiparticle weight for degenerate half - filled bands showing the Mott transition
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def plot_dop ( bands , int_max , dop , hund_cu , name ) : data = ssplt . calc_z ( bands , dop , np . arange ( 0 , int_max , 0.1 ) , hund_cu , name ) ssplt . plot_curves_z ( data , name )
Plot of Quasiparticle weight for N degenerate bands under selected doping shows transition only at half - fill the rest are metallic states
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def plot_dop_phase ( bands , int_max , hund_cu ) : name = 'Z_dop_phase_' + str ( bands ) + 'bands_U' + str ( int_max ) + 'J' + str ( hund_cu ) dop = np . sort ( np . hstack ( ( np . linspace ( 0.01 , 0.99 , 50 ) , np . arange ( 1. / 2. / bands , 1 , 1 / 2 / bands ) ) ) ) data = ssplt . calc_z ( bands , dop , np . arang...
Phase plot of Quasiparticle weight for N degenerate bands under doping shows transition only at interger filling the rest are metallic states
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def _register_extensions ( self , namespace ) : extmanager = ExtensionManager ( 'extensions.classes.{}' . format ( namespace ) , propagate_map_exceptions = True ) if extmanager . extensions : extmanager . map ( util . register_extension_class , base = self ) extmanager = ExtensionManager ( 'extensions.methods.{}' . for...
Register any extensions under the given namespace .
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def acls ( self ) : if self . _acls is None : self . _acls = InstanceAcls ( instance = self ) return self . _acls
The instance bound ACLs operations layer .
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def all ( self ) : return self . _instance . _client . acls . all ( self . _instance . name )
Get all ACLs for this instance .
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def create ( self , cidr_mask , description , ** kwargs ) : return self . _instance . _client . acls . create ( self . _instance . name , cidr_mask , description , ** kwargs )
Create an ACL for this instance .
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def get ( self , acl ) : return self . _instance . _client . acls . get ( self . _instance . name , acl )
Get the ACL specified by ID belonging to this instance .
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def _VarintEncoder ( ) : local_chr = chr def EncodeVarint ( write , value ) : bits = value & 0x7f value >>= 7 while value : write ( 0x80 | bits ) bits = value & 0x7f value >>= 7 return write ( bits ) return EncodeVarint
Return an encoder for a basic varint value .
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def _SignedVarintEncoder ( ) : local_chr = chr def EncodeSignedVarint ( write , value ) : if value < 0 : value += ( 1 << 64 ) bits = value & 0x7f value >>= 7 while value : write ( 0x80 | bits ) bits = value & 0x7f value >>= 7 return write ( bits ) return EncodeSignedVarint
Return an encoder for a basic signed varint value .
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def match ( value , query ) : if type ( query ) in [ str , int , float , type ( None ) ] : return value == query elif type ( query ) == dict and len ( query . keys ( ) ) == 1 : for op in query : if op == "$eq" : return value == query [ op ] elif op == "$lt" : return value < query [ op ] elif op == "$lte" : return value...
Determine whether a value satisfies a query .
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def features_tags_parse_str_to_dict ( obj ) : features = obj [ 'features' ] for i in tqdm ( range ( len ( features ) ) ) : tags = features [ i ] [ 'properties' ] . get ( 'tags' ) if tags is not None : try : tags = json . loads ( "{" + tags . replace ( "=>" , ":" ) + "}" ) except : try : tags = eval ( "{" + tags . repla...
Parse tag strings of all features in the collection into a Python dictionary if possible .
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def features_keep_by_property ( obj , query ) : features_keep = [ ] for feature in tqdm ( obj [ 'features' ] ) : if all ( [ match ( feature [ 'properties' ] . get ( prop ) , qry ) for ( prop , qry ) in query . items ( ) ] ) : features_keep . append ( feature ) obj [ 'features' ] = features_keep return obj
Filter all features in a collection by retaining only those that satisfy the provided query .
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def features_keep_within_radius ( obj , center , radius , units ) : features_keep = [ ] for feature in tqdm ( obj [ 'features' ] ) : if all ( [ getattr ( geopy . distance . vincenty ( ( lat , lon ) , center ) , units ) < radius for ( lon , lat ) in geojson . utils . coords ( feature ) ] ) : features_keep . append ( fea...
Filter all features in a collection by retaining only those that fall within the specified radius .
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def features_keep_using_features ( obj , bounds ) : bounds_shapes = [ ( feature , shapely . geometry . shape ( feature [ 'geometry' ] ) ) for feature in tqdm ( bounds [ 'features' ] ) if feature [ 'geometry' ] is not None ] index = rtree . index . Index ( ) for i in tqdm ( range ( len ( bounds_shapes ) ) ) : ( feature ...
Filter all features in a collection by retaining only those that fall within the features in the second collection .
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def features_node_edge_graph ( obj ) : points = { } features = obj [ 'features' ] for feature in tqdm ( obj [ 'features' ] ) : for ( lon , lat ) in geojson . utils . coords ( feature ) : points . setdefault ( ( lon , lat ) , 0 ) points [ ( lon , lat ) ] += 1 points = [ p for ( p , c ) in points . items ( ) if c > 1 ] f...
Transform the features into a more graph - like structure by appropriately splitting LineString features into two - point edges that connect Point nodes .
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def get_table_info ( conn , tablename ) : r = conn . execute ( "pragma table_info('{}')" . format ( tablename ) ) ret = TableInfo ( ( ( row [ "name" ] , row ) for row in r ) ) return ret
Returns TableInfo object
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def early_warning ( iterable , name = 'this generator' ) : nxt = None prev = next ( iterable ) while 1 : try : nxt = next ( iterable ) except : warning ( ' {} is now empty' . format ( name ) ) yield prev break else : yield prev prev = nxt
This function logs an early warning that the generator is empty .
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def post ( self , data , request , id ) : if id : raise errors . MethodNotAllowed ( ) user = self . _dict_to_model ( data ) user . save ( ) return Response ( 201 , None , { 'Location' : '%s%d' % ( reverse ( 'user' ) , user . pk ) } )
Create a new resource using POST
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def get ( self , request , id ) : if id : return self . _get_one ( id ) else : return self . _get_all ( )
Get one user or all users
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def put ( self , data , request , id ) : if not id : raise errors . MethodNotAllowed ( ) userdata = self . _dict_to_model ( data ) userdata . pk = id try : userdata . save ( force_update = True ) except DatabaseError : raise errors . NotFound ( )
Update a single user .
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def delete ( self , request , id ) : if not id : raise errors . MethodNotAllowed ( ) try : models . User . objects . get ( pk = id ) . delete ( ) except models . User . DoesNotExist : pass
Delete a single user .
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def _get_one ( self , id ) : try : return self . _to_dict ( models . User . objects . get ( pk = id ) ) except models . User . DoesNotExist : raise errors . NotFound ( )
Get one user from db and turn into dict
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def _get_all ( self ) : return [ self . _to_dict ( row ) for row in models . User . objects . all ( ) ]
Get all users from db and turn into list of dicts
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def _dict_to_model ( self , data ) : try : user = models . User ( ** data ) except TypeError : raise errors . BadRequest ( ) else : return user
Create new user model instance based on the received data .
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def captures ( self , uuid , withTitles = False ) : picker = lambda x : x . get ( 'capture' , [ ] ) return self . _get ( ( uuid , ) , picker , withTitles = 'yes' if withTitles else 'no' )
Return the captures for a given uuid optional value withTitles = yes
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def uuid ( self , type , val ) : picker = lambda x : x . get ( 'uuid' , x ) return self . _get ( ( type , val ) , picker )
Return the item - uuid for a identifier
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def mods ( self , uuid ) : picker = lambda x : x . get ( 'mods' , { } ) return self . _get ( ( 'mods' , uuid ) , picker )
Return a mods record for a given uuid
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def get_i18n_day_name ( day_nb , display = 'short' , ln = None ) : ln = default_ln ( ln ) _ = gettext_set_language ( ln ) if display == 'short' : days = { 0 : _ ( "Sun" ) , 1 : _ ( "Mon" ) , 2 : _ ( "Tue" ) , 3 : _ ( "Wed" ) , 4 : _ ( "Thu" ) , 5 : _ ( "Fri" ) , 6 : _ ( "Sat" ) } else : days = { 0 : _ ( "Sunday" ) , 1 ...
Get the string representation of a weekday internationalized
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def get_i18n_month_name ( month_nb , display = 'short' , ln = None ) : ln = default_ln ( ln ) _ = gettext_set_language ( ln ) if display == 'short' : months = { 0 : _ ( "Month" ) , 1 : _ ( "Jan" ) , 2 : _ ( "Feb" ) , 3 : _ ( "Mar" ) , 4 : _ ( "Apr" ) , 5 : _ ( "May" ) , 6 : _ ( "Jun" ) , 7 : _ ( "Jul" ) , 8 : _ ( "Aug"...
Get a non - numeric representation of a month internationalized .
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def create_month_selectbox ( name , selected_month = 0 , ln = None ) : ln = default_ln ( ln ) out = "<select name=\"%s\">\n" % name for i in range ( 0 , 13 ) : out += "<option value=\"%i\"" % i if ( i == selected_month ) : out += " selected=\"selected\"" out += ">%s</option>\n" % get_i18n_month_name ( i , ln ) out += "...
Creates an HTML menu for month selection . Value of selected field is numeric .
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def parse_runtime_limit ( value , now = None ) : def extract_time ( value ) : value = _RE_RUNTIMELIMIT_HOUR . search ( value ) . groupdict ( ) return timedelta ( hours = int ( value [ 'hours' ] ) , minutes = int ( value [ 'minutes' ] ) ) def extract_weekday ( value ) : key = value [ : 3 ] . lower ( ) try : return { 'mo...
Parsing CLI option for runtime limit supplied as VALUE .
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def guess_datetime ( datetime_string ) : if CFG_HAS_EGENIX_DATETIME : try : return Parser . DateTimeFromString ( datetime_string ) . timetuple ( ) except ValueError : pass else : for format in ( None , '%x %X' , '%X %x' , '%Y-%M-%dT%h:%m:%sZ' ) : try : return time . strptime ( datetime_string , format ) except ValueErr...
Try to guess the datetime contained in a string of unknow format .
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def get_dst ( date_obj ) : dst = 0 if date_obj . year >= 1900 : tmp_date = time . mktime ( date_obj . timetuple ( ) ) dst = time . localtime ( tmp_date ) [ - 1 ] return dst
Determine if dst is locally enabled at this time
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def utc_to_localtime ( date_str , fmt = "%Y-%m-%d %H:%M:%S" , input_fmt = "%Y-%m-%dT%H:%M:%SZ" ) : date_struct = datetime . strptime ( date_str , input_fmt ) date_struct += timedelta ( hours = get_dst ( date_struct ) ) date_struct -= timedelta ( seconds = time . timezone ) return strftime ( fmt , date_struct )
Convert UTC to localtime
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def _handle_call ( self , actual_call , stubbed_call ) : self . _actual_calls . append ( actual_call ) use_call = stubbed_call or actual_call return use_call . return_value
Extends Stub call handling behavior to be callable by default .
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def formatted_args ( self ) : arg_reprs = list ( map ( repr , self . args ) ) kwarg_reprs = [ '%s=%s' % ( k , repr ( v ) ) for k , v in self . kwargs . items ( ) ] return '(%s)' % ', ' . join ( arg_reprs + kwarg_reprs )
Format call arguments as a string .
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def check ( self ) : for tool in ( 'cd-hit' , 'prank' , 'hmmbuild' , 'hmmpress' , 'hmmscan' , 'phmmer' , 'mafft' , 'meme' ) : if not self . pathfinder . exists ( tool ) : raise RuntimeError ( "Dependency {} is missing" . format ( tool ) )
Check if data and third party tools are available
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def generate_non_rabs ( self ) : logging . info ( 'Building non-Rab DB' ) run_cmd ( [ self . pathfinder [ 'cd-hit' ] , '-i' , self . path [ 'non_rab_db' ] , '-o' , self . output [ 'non_rab_db' ] , '-d' , '100' , '-c' , str ( config [ 'param' ] [ 'non_rab_db_identity_threshold' ] ) , '-g' , '1' , '-T' , self . cpu ] ) o...
Shrink the non - Rab DB size by reducing sequence redundancy .
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def parse_duration ( duration ) : duration = str ( duration ) . upper ( ) . strip ( ) elements = ELEMENTS . copy ( ) for pattern in ( SIMPLE_DURATION , COMBINED_DURATION ) : if pattern . match ( duration ) : found = pattern . match ( duration ) . groupdict ( ) del found [ 'time' ] elements . update ( dict ( ( k , int (...
Attepmts to parse an ISO8601 formatted duration .
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def skin_details ( skin_id , lang = "en" ) : params = { "skin_id" : skin_id , "lang" : lang } cache_name = "skin_details.%(skin_id)s.%(lang)s.json" % params return get_cached ( "skin_details.json" , cache_name , params = params )
This resource returns details about a single skin .
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def bubble_to_gexf ( bblfile : str , gexffile : str = None , oriented : bool = False ) : tree = BubbleTree . from_bubble_file ( bblfile , oriented = bool ( oriented ) ) gexf_converter . tree_to_file ( tree , gexffile ) return gexffile
Write in bblfile a graph equivalent to those depicted in bubble file
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def bubble_to_js ( bblfile : str , jsdir : str = None , oriented : bool = False , ** style ) : js_converter . bubble_to_dir ( bblfile , jsdir , oriented = bool ( oriented ) , ** style ) return jsdir
Write in jsdir a graph equivalent to those depicted in bubble file
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def tree_to_graph ( bbltree : BubbleTree ) -> Graph or Digraph : GraphObject = Digraph if bbltree . oriented else Graph def create ( name : str ) : ret = GraphObject ( 'cluster_' + name ) ret . node ( name , style = 'invis' , shape = 'point' ) ret . body . append ( 'color=lightgrey' ) ret . body . append ( 'label=""' )...
Compute as a graphviz . Graph instance the given graph .
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def to_dict ( self ) : ret = OrderedDict ( ) for attrname in self . attrs : ret [ attrname ] = self . __getattribute__ ( attrname ) return ret
Returns OrderedDict whose keys are self . attrs
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def to_list ( self ) : ret = OrderedDict ( ) for attrname in self . attrs : ret [ attrname ] = self . __getattribute__ ( attrname ) return ret
Returns list containing values of attributes listed in self . attrs
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def uniq ( pipe ) : pipe = iter ( pipe ) previous = next ( pipe ) yield previous for i in pipe : if i is not previous : previous = i yield i
this works like bash s uniq command where the generator only iterates if the next value is not the previous
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def send_request ( url , method , data , args , params , headers , cookies , timeout , is_json , verify_cert ) : for p in args : url = url . replace ( ':' + p , str ( args [ p ] ) ) try : if data : if is_json : headers [ 'Content-Type' ] = 'application/json' data = json . dumps ( data ) request = requests . Request ( m...
Forge and send HTTP request .
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def neighbors ( self ) -> List [ 'Node' ] : self . _load_neighbors ( ) return [ edge . source if edge . source != self else edge . target for edge in self . _neighbors . values ( ) ]
The list of neighbors of the node .
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def _load_neighbors ( self ) -> None : if not self . are_neighbors_cached : self . _load_neighbors_from_external_source ( ) db : GraphDatabaseInterface = self . _graph . database db_node : DBNode = db . Node . find_by_name ( self . name ) db_node . are_neighbors_cached = True db . session . commit ( ) self . are_neighb...
Loads all neighbors of the node from the local database and from the external data source if needed .
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def _load_neighbors_from_database ( self ) -> None : self . _are_neighbors_loaded = True graph : Graph = self . _graph neighbors : List [ DBNode ] = graph . database . Node . find_by_name ( self . name ) . neighbors nodes : NodeList = graph . nodes for db_node in neighbors : graph . add_node ( db_node . name , db_node ...
Loads the neighbors of the node from the local database .
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def key ( self ) -> Tuple [ int , int ] : return self . _source . index , self . _target . index
The unique identifier of the edge consisting of the indexes of its source and target nodes .
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def edge_list ( self ) -> List [ Edge ] : return [ edge for edge in sorted ( self . _edges . values ( ) , key = attrgetter ( "key" ) ) ]
The ordered list of edges in the container .
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def beforeSummaryReport ( self , event ) : self . prof . disable ( ) stats = pstats . Stats ( self . prof , stream = event . stream ) . sort_stats ( self . sort ) event . stream . writeln ( nose2 . util . ln ( 'Profiling results' ) ) stats . print_stats ( ) if self . pfile : stats . dump_stats ( self . pfile ) if self ...
Output profiling results
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def separate ( text ) : alphabet = 'abcdefghijklmnopqrstuvwxyz' words = text . split ( ) standardwords = [ ] for word in words : newstr = '' for char in word : if char in alphabet or char in alphabet . upper ( ) : newstr += char if newstr != '' : standardwords . append ( newstr ) return map ( lambda x : x . lower ( ) ,...
Takes text and separates it into a list of words