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def _logout ( self , reset = True ) : url = '{base}/client/auth/logout' . format ( base = self . base_url ) response = self . _session . get ( url , params = self . _parameters ) if response . ok : if reset : self . _reset ( ) return True else : return False
Log out of the API .
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def _state ( self ) : state = { } required_keys = ( 'deviceStatusInfo' , 'gasUsage' , 'powerUsage' , 'thermostatInfo' , 'thermostatStates' ) try : for _ in range ( self . _state_retries ) : state . update ( self . _get_data ( '/client/auth/retrieveToonState' ) ) except TypeError : self . _logger . exception ( 'Could no...
The internal state of the object .
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def get_smokedetector_by_name ( self , name ) : return next ( ( smokedetector for smokedetector in self . smokedetectors if smokedetector . name . lower ( ) == name . lower ( ) ) , None )
Retrieves a smokedetector object by its name
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def get_light_by_name ( self , name ) : return next ( ( light for light in self . lights if light . name . lower ( ) == name . lower ( ) ) , None )
Retrieves a light object by its name
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def get_smartplug_by_name ( self , name ) : return next ( ( plug for plug in self . smartplugs if plug . name . lower ( ) == name . lower ( ) ) , None )
Retrieves a smartplug object by its name
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def get_thermostat_state_by_name ( self , name ) : self . _validate_thermostat_state_name ( name ) return next ( ( state for state in self . thermostat_states if state . name . lower ( ) == name . lower ( ) ) , None )
Retrieves a thermostat state object by its assigned name
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def get_thermostat_state_by_id ( self , id_ ) : return next ( ( state for state in self . thermostat_states if state . id == id_ ) , None )
Retrieves a thermostat state object by its id
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def thermostat_state ( self ) : current_state = self . thermostat_info . active_state state = self . get_thermostat_state_by_id ( current_state ) if not state : self . _logger . debug ( 'Manually set temperature, no Thermostat ' 'State chosen!' ) return state
The state of the thermostat programming
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def thermostat_state ( self , name ) : self . _validate_thermostat_state_name ( name ) id_ = next ( ( key for key in STATES . keys ( ) if STATES [ key ] . lower ( ) == name . lower ( ) ) , None ) data = copy . copy ( self . _parameters ) data . update ( { 'state' : 2 , 'temperatureState' : id_ } ) response = self . _ge...
Changes the thermostat state to the one passed as an argument as name
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def thermostat ( self , temperature ) : target = int ( temperature * 100 ) data = copy . copy ( self . _parameters ) data . update ( { 'value' : target } ) response = self . _get_data ( '/client/auth/setPoint' , data ) self . _logger . debug ( 'Response received {}' . format ( response ) ) self . _clear_cache ( )
A temperature to set the thermostat to . Requires a float .
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def euler_tour_dfs ( G , source = None ) : if source is None : # produce edges for all components nodes = G else : # produce edges for components with source nodes = [ source ] yielder = [ ] visited = set ( ) for start in nodes : if start in visited : continue visited . add ( start ) stack = [ ( start , iter ( G [ star...
adaptation of networkx dfs
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def reroot ( self , s ) : # Splice out the first part of the sequence ending with the occurrence before os # remove its first occurrence (or), o_s1 = self . first_lookup [ s ] splice1 = self . tour [ 1 : o_s1 ] rest = self . tour [ o_s1 + 1 : ] new_tour = [ s ] + rest + splice1 + [ s ] new_tree = TestETT . from_tour ( ...
s = 3 s = B
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def remove_edge ( self , u , v ) : # Remove (u, v) from represented graph print ( 'Dynamically removing uv=(%r, %r)' % ( u , v ) ) self . graph . remove_edge ( u , v ) e = ( u , v ) # Remove edge e = (u, v) from all graphs. if not self . forests [ 0 ] . has_edge ( u , v ) : # If (u, v) is a non-tree edge, simply delete...
Using notation where 0 is top level
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def extend_regex2 ( regexpr , reflags = 0 ) : regexpr = extend_regex ( regexpr ) IGNORE_CASE_PREF = '\\c' if regexpr . startswith ( IGNORE_CASE_PREF ) : # hack for vim-like ignore case regexpr = regexpr [ len ( IGNORE_CASE_PREF ) : ] reflags = reflags | re . IGNORECASE return regexpr , reflags
also preprocesses flags
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def named_field ( key , regex , vim = False ) : if key is None : #return regex return r'(%s)' % ( regex , ) if vim : return r'\(%s\)' % ( regex ) else : return r'(?P<%s>%s)' % ( key , regex )
Creates a named regex group that can be referend via a backref . If key is None the backref is referenced by number .
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def regex_replace ( regex , repl , text ) : return re . sub ( regex , repl , text , * * RE_KWARGS )
r thin wrapper around re . sub regex_replace
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def clear ( prompt = True , cache = None ) : cache = cache or config . cache ( ) if prompt : answer = input ( 'Clear library cache files in %s/? (yN) ' % cache ) if not answer . startswith ( 'y' ) : return False shutil . rmtree ( cache , ignore_errors = True ) return True
Clear loady s cache .
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def create ( gitpath , cache = None ) : if gitpath . startswith ( config . LIBRARY_PREFIX ) : path = gitpath [ len ( config . LIBRARY_PREFIX ) : ] return Library ( * path . split ( '/' ) , cache = cache )
Create a Library from a git path .
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def load ( self ) : if not git : raise EnvironmentError ( MISSING_GIT_ERROR ) if os . path . exists ( self . path ) : if not config . CACHE_DISABLE : return shutil . rmtree ( self . path , ignore_errors = True ) with files . remove_on_exception ( self . path ) : url = self . GIT_URL . format ( * * vars ( self ) ) repo ...
Load the library .
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def check_existens_of_staging_tag_in_remote_repo ( ) : staging_tag = Git . create_git_version_tag ( APISettings . GIT_STAGING_PRE_TAG ) command_git = 'git ls-remote -t' command_awk = 'awk \'{print $2}\'' command_cut_1 = 'cut -d \'/\' -f 3' command_cut_2 = 'cut -d \'^\' -f 1' command_sort = 'sort -b -t . -k 1,1nr -k 2,2...
This method will check if the given tag exists as a staging tag in the remote repository .
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def __debug ( command , dry = False ) : if dry : command . append ( '--dry-run' ) Shell . debug ( command ) if dry : call ( command ) exit ( 1 )
This method will be called if the debug mode is on .
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def __git_add ( args = '' ) : command = [ 'git' , 'add' , '.' ] Shell . msg ( 'Adding files...' ) if APISettings . DEBUG : Git . __debug ( command , True ) for key in args : command . append ( key ) if not call ( command ) : pass return False
Add files to staging . The function call will return 0 if the command success .
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def __git_commit ( git_tag ) : Shell . msg ( 'Commit changes.' ) if APISettings . DEBUG : Shell . debug ( 'Execute "git commit" in dry mode.' ) if not call ( [ 'git' , 'commit' , '-m' , '\'' + git_tag + '\'' , '--dry-run' ] ) : pass return True if not call ( [ 'git' , 'commit' , '-m' , '\'' + git_tag + '\'' ] ) : retur...
Commit files to branch . The function call will return 0 if the command success .
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def __git_tag ( git_tag ) : command = [ 'git' , 'tag' , '-a' , git_tag , '-m' , '\'' + git_tag + '\'' ] Shell . msg ( 'Create tag from version ' + git_tag ) if APISettings . DEBUG : Git . __debug ( command , False ) if not call ( command ) : return True return False
Create new tag . The function call will return 0 if the command success .
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def __git_tag_push ( ) : command = [ 'git' , 'push' , 'origin' , '--tags' ] Shell . msg ( 'Pushing tags...' ) if APISettings . DEBUG : Git . __debug ( command , True ) if not call ( command ) : return True return False
Push all tags . The function call will return 0 if the command success .
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def split_into_batches ( input_list , batch_size , batch_storage_dir , checkpoint = False ) : if checkpoint and not os . path . exists ( batch_storage_dir ) : os . mkdir ( batch_storage_dir ) batches = [ { 'index' : batch_index , 'data' : input_list [ start_index : start_index + batch_size ] , 'input_filename' : os . p...
Break the input data into smaller batches optionally saving each one to disk .
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def map_batch_parallel ( input_list , batch_size , item_mapper = None , batch_mapper = None , flatten = True , n_jobs = - 1 , * * kwargs ) : # We must specify either how to process each batch or how to process each item. if item_mapper is None and batch_mapper is None : raise ValueError ( 'You should specify either bat...
Split the data into batches and process each batch in its own thread .
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def get_cfg ( ast_func ) : cfg_func = cfg . Function ( ) for ast_var in ast_func . input_variable_list : cfg_var = cfg_func . get_variable ( ast_var . name ) cfg_func . add_input_variable ( cfg_var ) for ast_var in ast_func . output_variable_list : cfg_var = cfg_func . get_variable ( ast_var . name ) cfg_func . add_out...
Traverses the AST and returns the corresponding CFG
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def overrideable_partial ( func , * args , * * default_kwargs ) : import functools @ functools . wraps ( func ) def partial_wrapper ( * given_args , * * given_kwargs ) : kwargs = default_kwargs . copy ( ) kwargs . update ( given_kwargs ) return func ( * ( args + given_args ) , * * kwargs ) return partial_wrapper
like partial but given kwargs can be overrideden at calltime
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def get_nonconflicting_string ( base_fmtstr , conflict_set , offset = 0 ) : # Infinite loop until we find a non-conflict conflict_set_ = set ( conflict_set ) for count in it . count ( offset ) : base_str = base_fmtstr % count if base_str not in conflict_set_ : return base_str
gets a new string that wont conflict with something that already exists
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def get_nonconflicting_path_old ( base_fmtstr , dpath , offset = 0 ) : import utool as ut from os . path import basename pattern = '*' dname_list = ut . glob ( dpath , pattern , recursive = False , with_files = True , with_dirs = True ) conflict_set = set ( [ basename ( dname ) for dname in dname_list ] ) newname = ut ...
r base_fmtstr must have a %d in it
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def are_you_sure ( msg = '' ) : print ( msg ) from utool import util_arg from utool import util_str override = util_arg . get_argflag ( ( '--yes' , '--y' , '-y' ) ) if override : print ( 'accepting based on command line flag' ) return True valid_ans = [ 'yes' , 'y' ] valid_prompt = util_str . conj_phrase ( valid_ans , ...
r Prompts user to accept or checks command line for - y
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def grace_period ( msg = '' , seconds = 10 ) : import time print ( msg ) override = util_arg . get_argflag ( ( '--yes' , '--y' , '-y' ) ) print ( 'starting grace period' ) if override : print ( 'ending based on command line flag' ) return True for count in reversed ( range ( 1 , seconds + 1 ) ) : time . sleep ( 1 ) pri...
Gives user a window to stop a process before it happens
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def delayed_retry_gen ( delay_schedule = [ .1 , 1 , 10 ] , msg = None , timeout = None , raise_ = True ) : import utool as ut import time if not ut . isiterable ( delay_schedule ) : delay_schedule = [ delay_schedule ] tt = ut . tic ( ) # First attempt is immediate yield 0 for count in it . count ( 0 ) : #print('count =...
template code for a infinte retry loop
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def get_stats_str ( list_ = None , newlines = False , keys = None , exclude_keys = [ ] , lbl = None , precision = None , axis = 0 , stat_dict = None , use_nan = False , align = False , use_median = False , * * kwargs ) : from utool . util_str import repr4 import utool as ut # Get stats dict if stat_dict is None : stat_...
Returns the string version of get_stats
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def make_call_graph ( func , * args , * * kwargs ) : from pycallgraph import PyCallGraph from pycallgraph . output import GraphvizOutput with PyCallGraph ( output = GraphvizOutput ) : func ( * args , * * kwargs )
profile with pycallgraph
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def _memory_profile ( with_gc = False ) : import utool as ut if with_gc : garbage_collect ( ) import guppy hp = guppy . hpy ( ) print ( '[hpy] Waiting for heap output...' ) heap_output = hp . heap ( ) print ( heap_output ) print ( '[hpy] total heap size: ' + ut . byte_str2 ( heap_output . size ) ) ut . util_resources ....
Helper for memory debugging . Mostly just a namespace where I experiment with guppy and heapy .
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def make_object_graph ( obj , fpath = 'sample_graph.png' ) : import objgraph objgraph . show_most_common_types ( ) #print(objgraph.by_type('ndarray')) #objgraph.find_backref_chain( # random.choice(objgraph.by_type('ndarray')), # objgraph.is_proper_module) objgraph . show_refs ( [ obj ] , filename = 'ref_graph.png' ) ob...
memoryprofile with objgraph
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def inverable_unique_two_lists ( item1_list , item2_list ) : import utool as ut unique_list1 , inverse1 = np . unique ( item1_list , return_inverse = True ) unique_list2 , inverse2 = np . unique ( item2_list , return_inverse = True ) flat_stacked , cumsum = ut . invertible_flatten2 ( ( unique_list1 , unique_list2 ) ) f...
item1_list = aid1_list item2_list = aid2_list
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def uninvert_unique_two_lists ( flat_list , reconstruct_tup ) : import utool as ut ( inverse3 , cumsum , inverse2 , inverse1 ) = reconstruct_tup flat_stacked_ = ut . take ( flat_list , inverse3 ) unique_list1_ , unique_list2_ = ut . unflatten2 ( flat_stacked_ , cumsum ) res_list1_ = ut . take ( unique_list1_ , inverse1...
flat_list = thumb_list
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def search_module ( mod , pat , ignore_case = True , recursive = False , _seen = None ) : if _seen is not None and mod in _seen : return [ ] import utool as ut reflags = re . IGNORECASE * ignore_case found_list = [ name for name in dir ( mod ) if re . search ( pat , name , flags = reflags ) ] if recursive : if _seen is...
r Searches module functions classes and constants for members matching a pattern .
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def instancelist ( obj_list , check = False , shared_attrs = None ) : class InstanceList_ ( object ) : def __init__ ( self , obj_list , shared_attrs = None ) : self . _obj_list = [ ] self . _shared_public_attrs = [ ] self . _example_type = None if len ( obj_list ) > 0 : import utool as ut self . _obj_list = obj_list ex...
Executes methods and attribute calls on a list of objects of the same type
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def _heappush_max ( heap , item ) : heap . append ( item ) heapq . _siftdown_max ( heap , 0 , len ( heap ) - 1 )
why is this not in heapq
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def take_column ( self , keys , * extra_keys ) : import utool as ut keys = ut . ensure_iterable ( keys ) + list ( extra_keys ) key_to_list = ut . dict_subset ( self . _key_to_list , keys ) newself = self . __class__ ( key_to_list , self . _meta . copy ( ) ) return newself
Takes a subset of columns
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def take ( self , idxs ) : import utool as ut if False : key_to_list = ut . odict ( [ ( key , ut . take ( val , idxs ) ) for key , val in six . iteritems ( self . _key_to_list ) ] ) else : import numpy as np key_to_list = ut . odict ( [ ( key , ut . take ( val , idxs ) ) if not isinstance ( val , np . ndarray ) else va...
Takes a subset of rows
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def remove ( self , idxs ) : import utool as ut keep_idxs = ut . index_complement ( idxs , len ( self ) ) return self . take ( keep_idxs )
Returns a copy with idxs removed
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def group_items ( self , labels ) : import utool as ut unique_labels , groups = self . group ( labels ) label_to_group = ut . odict ( zip ( unique_labels , groups ) ) return label_to_group
group as dict
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def group ( self , labels ) : unique_labels , groupxs = self . group_indicies ( labels ) groups = [ self . take ( idxs ) for idxs in groupxs ] return unique_labels , groups
group as list
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3
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def cast_column ( self , keys , func ) : import utool as ut for key in ut . ensure_iterable ( keys ) : self [ key ] = [ func ( v ) for v in self [ key ] ]
like map column but applies values inplace
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def merge_rows ( self , key , merge_scalars = True ) : import utool as ut unique_labels , groupxs = self . group_indicies ( key ) single_xs = [ xs for xs in groupxs if len ( xs ) == 1 ] multi_xs = [ xs for xs in groupxs if len ( xs ) > 1 ] singles = self . take ( ut . flatten ( single_xs ) ) multis = [ self . take ( id...
Uses key as a unique index an merges all duplicates rows . Use cast_column to modify types of columns before merging to affect behavior of duplicate rectification .
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def peek ( self ) : # Ammortized O(1) _heap = self . _heap _dict = self . _dict val , key = _heap [ 0 ] # Remove items marked for lazy deletion as they are encountered while key not in _dict or _dict [ key ] != val : self . _heappop ( _heap ) val , key = _heap [ 0 ] return key , val
Peek at the next item in the queue
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def peek_many ( self , n ) : if n == 0 : return [ ] elif n == 1 : return [ self . peek ( ) ] else : items = list ( self . pop_many ( n ) ) self . update ( items ) return items
Actually this can be quite inefficient
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def pop ( self , key = util_const . NoParam , default = util_const . NoParam ) : # Dictionary pop if key is specified if key is not util_const . NoParam : if default is util_const . NoParam : return ( key , self . _dict . pop ( key ) ) else : return ( key , self . _dict . pop ( key , default ) ) # Otherwise do a heap p...
Pop the next item off the queue
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def __execute_fromimport ( module , modname , import_tuples , verbose = False ) : if verbose : print ( '[UTIL_IMPORT] EXECUTING %d FROM IMPORT TUPLES' % ( len ( import_tuples ) , ) ) from_imports = __get_from_imports ( import_tuples ) for name , fromlist in from_imports : full_modname = '.' . join ( ( modname , name ) ...
Module From Imports
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def _initstr ( modname , imports , from_imports , inject_execstr , withheader = True ) : header = _make_module_header ( ) if withheader else '' import_str = _make_imports_str ( imports , modname ) fromimport_str = _make_fromimport_str ( from_imports , modname ) initstr = '\n' . join ( [ str_ for str_ in [ header , impo...
Calls the other string makers
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def _inject_execstr ( modname , import_tuples ) : if modname == 'utool' : # Special case import of the util_inject module injecter = 'util_inject' injecter_import = '' else : # Normal case implicit import of util_inject injecter_import = 'import utool' injecter = 'utool' injectstr_fmt = textwrap . dedent ( r''' # START...
Injection and Reload String Defs
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def make_initstr ( modname , import_tuples , verbose = False ) : imports = [ tup [ 0 ] for tup in import_tuples ] from_imports = __get_from_imports ( import_tuples ) inject_execstr = _inject_execstr ( modname , import_tuples ) return _initstr ( modname , imports , from_imports , inject_execstr )
Just creates the string representation . Does no importing .
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def make_import_tuples ( module_path , exclude_modnames = [ ] ) : from utool import util_path kwargs = dict ( private = False , full = False ) module_list = util_path . ls_modulefiles ( module_path , noext = True , * * kwargs ) package_list = util_path . ls_moduledirs ( module_path , * * kwargs ) exclude_set = set ( ex...
Infer the import_tuples from a module_path
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def get_resource_dir ( ) : #resource_prefix = '~' if WIN32 : dpath_ = '~/AppData/Roaming' elif LINUX : dpath_ = '~/.config' elif DARWIN : dpath_ = '~/Library/Application Support' else : raise AssertionError ( 'unknown os' ) dpath = normpath ( expanduser ( dpath_ ) ) return dpath
Returns a directory which should be writable for any application
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def load_data ( fpath , * * kwargs ) : ext = splitext ( fpath ) [ 1 ] if ext in [ '.pickle' , '.cPkl' , '.pkl' ] : return load_cPkl ( fpath , * * kwargs ) elif ext in [ '.json' ] : return load_json ( fpath , * * kwargs ) elif ext in [ '.hdf5' ] : return load_hdf5 ( fpath , * * kwargs ) elif ext in [ '.txt' ] : return l...
More generic interface to load data
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def save_data ( fpath , data , * * kwargs ) : ext = splitext ( fpath ) [ 1 ] if ext in [ '.pickle' , '.cPkl' , '.pkl' ] : return save_cPkl ( fpath , data , * * kwargs ) elif ext in [ '.json' ] : return save_json ( fpath , data , * * kwargs ) elif ext in [ '.hdf5' ] : return save_hdf5 ( fpath , data , * * kwargs ) elif ...
More generic interface to write data
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def write_to ( fpath , to_write , aslines = False , verbose = None , onlyifdiff = False , mode = 'w' , n = None ) : if onlyifdiff : import utool as ut if ut . hashstr ( read_from ( fpath ) ) == ut . hashstr ( to_write ) : print ( '[util_io] * no difference' ) return verbose = _rectify_verb_write ( verbose ) if verbose ...
Writes text to a file . Automatically encodes text as utf8 .
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def read_from ( fpath , verbose = None , aslines = False , strict = True , n = None , errors = 'replace' ) : if n is None : n = __READ_TAIL_N__ verbose = _rectify_verb_read ( verbose ) if verbose : print ( '[util_io] * Reading text file: %r ' % util_path . tail ( fpath , n = n ) ) try : if not util_path . checkpath ( f...
r Reads text from a file . Automatically returns utf8 .
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def save_cPkl ( fpath , data , verbose = None , n = None ) : verbose = _rectify_verb_write ( verbose ) if verbose : print ( '[util_io] * save_cPkl(%r, data)' % ( util_path . tail ( fpath , n = n ) , ) ) with open ( fpath , 'wb' ) as file_ : # Use protocol 2 to support python2 and 3 pickle . dump ( data , file_ , protoc...
Saves data to a pickled file with optional verbosity
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def load_cPkl ( fpath , verbose = None , n = None ) : verbose = _rectify_verb_read ( verbose ) if verbose : print ( '[util_io] * load_cPkl(%r)' % ( util_path . tail ( fpath , n = n ) , ) ) try : with open ( fpath , 'rb' ) as file_ : data = pickle . load ( file_ ) except UnicodeDecodeError : if six . PY3 : # try to open...
Loads a pickled file with optional verbosity . Aims for compatibility between python2 and python3 .
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def save_hdf5 ( fpath , data , verbose = None , compression = 'lzf' ) : import h5py verbose = _rectify_verb_write ( verbose ) if verbose : print ( '[util_io] * save_hdf5(%r, data)' % ( util_path . tail ( fpath ) , ) ) if verbose > 1 : if isinstance ( data , dict ) : print ( '[util_io] ... shapes=%r' % ( [ val . shape f...
r Restricted save of data using hdf5 . Can only save ndarrays and dicts of ndarrays .
730
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def save_pytables ( fpath , data , verbose = False ) : import tables #from os.path import basename #fname = basename(fpath) #shape = data.shape #dtype = data.dtype #file_ = tables.open_file(fpath) verbose = _rectify_verb_write ( verbose ) if verbose : print ( '[util_io] * save_pytables(%r, data)' % ( util_path . tail (...
sudo pip install numexpr sudo pip install tables
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def start_simple_webserver ( domain = None , port = 5832 ) : import tornado . ioloop import tornado . web import tornado . httpserver import tornado . wsgi import flask app = flask . Flask ( '__simple__' ) @ app . route ( '/' , methods = [ 'GET' , 'POST' , 'DELETE' , 'PUT' ] ) def echo_args ( * args , * * kwargs ) : fr...
r simple webserver that echos its arguments
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def render_html ( html_str ) : import utool as ut from os . path import abspath import webbrowser try : html_str = html_str . decode ( 'utf8' ) except Exception : pass html_dpath = ut . ensure_app_resource_dir ( 'utool' , 'temp_html' ) fpath = abspath ( ut . unixjoin ( html_dpath , 'temp.html' ) ) url = 'file://' + fpa...
makes a temporary html rendering
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def publish ( func ) : @ wraps ( func ) def wrapper ( self , * args , * * kwargs ) : # outgoing payload = func ( self , * args , * * kwargs ) payload . pop ( 'self' , None ) self . _publish ( func . __name__ , payload ) return None wrapper . is_publish = True return wrapper
publish the return value of this function as a message from this endpoint
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def request ( func = None , timeout = 600 ) : if func is None : return partial ( request , timeout = timeout ) @ wraps ( func ) def wrapper ( self , * args , * * kwargs ) : params = func ( self , * args , * * kwargs ) self = params . pop ( 'self' , None ) entity = params . pop ( 'entity' , None ) app_name = params . po...
use to request an api call from a specific endpoint
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def serialize_problem ( req , resp , problem ) : preferred = req . client_prefers ( ( 'application/json' , 'application/problem+json' ) ) if preferred is None : preferred = 'application/json' resp . data = problem . to_json ( ) . encode ( 'utf-8' ) resp . content_type = preferred resp . append_header ( 'Vary' , 'Accept...
Serialize the given instance of Problem .
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def add_psms_to_proteindata ( proteindata , p_acc , pool , psmdata ) : seq , psm_id = psmdata [ 2 ] , psmdata [ 3 ] try : proteindata [ p_acc ] [ 'pools' ] [ pool ] [ 'psms' ] . add ( psm_id ) except KeyError : emptyinfo = { 'psms' : set ( ) , 'peptides' : set ( ) , 'unipeps' : 0 } try : proteindata [ p_acc ] [ 'pools'...
Fill function for create_featuredata_map
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def print_traceback ( with_colors = True ) : #traceback.print_tb() import traceback stack = traceback . extract_stack ( ) stack_lines = traceback . format_list ( stack ) tbtext = '' . join ( stack_lines ) if with_colors : try : from pygments import highlight from pygments . lexers import get_lexer_by_name from pygments...
prints current stack
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def is_valid_varname ( varname ) : if not isinstance ( varname , six . string_types ) : return False match_obj = re . match ( varname_regex , varname ) valid_syntax = match_obj is not None valid_name = not keyword . iskeyword ( varname ) isvalid = valid_syntax and valid_name return isvalid
Checks syntax and validity of a variable name
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def execstr_dict ( dict_ , local_name = None , exclude_list = None , explicit = False ) : import utool as ut if explicit : expr_list = [ ] for ( key , val ) in sorted ( dict_ . items ( ) ) : assert isinstance ( key , six . string_types ) , 'keys must be strings' expr_list . append ( '%s = %s' % ( key , ut . repr2 ( val...
returns execable python code that declares variables using keys and values
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def embed2 ( * * kwargs ) : config = kwargs . get ( 'config' ) header = kwargs . pop ( 'header' , u'' ) stack_depth = kwargs . pop ( 'stack_depth' , 2 ) compile_flags = kwargs . pop ( 'compile_flags' , None ) import IPython from IPython . core . interactiveshell import InteractiveShell from IPython . terminal . embed i...
Modified from IPython . terminal . embed . embed so I can mess with stack_depth
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def search_stack_for_localvar ( varname ) : curr_frame = inspect . currentframe ( ) print ( ' * Searching parent frames for: ' + six . text_type ( varname ) ) frame_no = 0 while curr_frame . f_back is not None : if varname in curr_frame . f_locals . keys ( ) : print ( ' * Found in frame: ' + six . text_type ( frame_no ...
Finds a local varable somewhere in the stack and returns the value
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def formatex ( ex , msg = '[!?] Caught exception' , prefix = None , key_list = [ ] , locals_ = None , iswarning = False , tb = False , N = 0 , keys = None , colored = None ) : # Get error prefix and local info if prefix is None : prefix = get_caller_prefix ( aserror = True , N = N ) if locals_ is None : locals_ = get_p...
r Formats an exception with relevant info
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def parse_locals_keylist ( locals_ , key_list , strlist_ = None , prefix = '' ) : from utool import util_str if strlist_ is None : strlist_ = [ ] for key in key_list : try : if key is None : strlist_ . append ( '' ) elif isinstance ( key , tuple ) : # Given a tuple of information tup = key func , key_ = tup val = get_v...
For each key in keylist puts its value in locals into a stringlist
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def switch_psm_to_peptable_fields ( oldheader ) : return { old : new for old , new in zip ( [ mzidtsvdata . HEADER_PEPTIDE , mzidtsvdata . HEADER_PROTEIN , mzidtsvdata . HEADER_PEPTIDE_Q , mzidtsvdata . HEADER_PEPTIDE_PEP ] , [ peptabledata . HEADER_PEPTIDE , peptabledata . HEADER_PROTEINS , peptabledata . HEADER_QVAL ...
Returns a dict map with old to new header fields
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def add_instruction ( self , instr ) : assert ( isinstance ( instr , Instruction ) ) self . instruction_list . append ( instr ) if instr . lhs not in self . defined_variables : if isinstance ( instr . lhs , Variable ) : self . defined_variables . append ( instr . lhs ) if isinstance ( instr , EqInstruction ) : if isins...
Adds the argument instruction in the list of instructions of this basic block .
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def set_condition ( self , condition , condition_instr = None ) : assert ( isinstance ( condition , Numeric ) ) if condition_instr is not None : assert ( isinstance ( condition_instr , CmpInstruction ) ) self . condition = condition self . condition_instr = condition_instr if condition_instr is not None : if condition_...
Defines the condition which decides how the basic block exits
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def add_basic_block ( self , basic_block ) : assert ( isinstance ( basic_block , BasicBlock ) ) self . basic_block_list . append ( basic_block )
Adds the given basic block in the function
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def get_variable ( self , var_name ) : assert ( isinstance ( var_name , str ) ) if isinstance ( var_name , str ) : for var in self . variable_list : if var . name == var_name : return var new_var = Variable ( var_name ) self . variable_list . append ( new_var ) return new_var
If a variable with the name var_name exists in this function s variable list \ then that variable object is returned ; else a new variable is created \ with the given name and added to the variable list of this function \ and returned back
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def add_input_variable ( self , var ) : assert ( isinstance ( var , Variable ) ) self . input_variable_list . append ( var )
Adds the argument variable as one of the input variable
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def add_output_variable ( self , var ) : assert ( isinstance ( var , Variable ) ) self . output_variable_list . append ( var )
Adds the argument variable as one of the output variable
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def tokenize ( self ) : self . token_list = [ ] ps = self . parse_string . strip ( ) i = 0 last_token = None while i < len ( ps ) and ps [ i ] . isspace ( ) : i += 1 while i < len ( ps ) : token = '' if ps [ i ] . isalpha ( ) : while i < len ( ps ) and ( ps [ i ] . isalnum ( ) or ps [ i ] == '_' ) : token += ps [ i ] i...
Tokenizes the string stored in the parser object into a list of tokens .
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def parse ( self ) : #print("Parsing: %s"%self.parse_string) self . tokenize ( ) if self . debug : print ( "Tokens found: %s" % self . token_list ) try : parse_tree = self . parse2 ( ) except Exception as e : raise e return parse_tree
Tokenizes and parses an arithmetic expression into a parse tree .
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def insert_keys ( self , keys ) : start = 0 bulk_insert = self . bulk_insert keys_len = len ( keys ) query = 'INSERT IGNORE INTO gauged_keys (namespace, `key`) VALUES ' execute = self . cursor . execute while start < keys_len : rows = keys [ start : start + bulk_insert ] params = [ param for params in rows for param in...
Insert keys into a table which assigns an ID
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def get_writer_position ( self , name ) : cursor = self . cursor cursor . execute ( 'SELECT timestamp FROM gauged_writer_history ' 'WHERE id = %s' , ( name , ) ) result = cursor . fetchone ( ) return result [ 0 ] if result else 0
Get the current writer position
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def get_namespaces ( self ) : cursor = self . cursor cursor . execute ( 'SELECT DISTINCT namespace FROM gauged_statistics' ) return [ namespace for namespace , in cursor ]
Get a list of namespaces
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def remove_namespace ( self , namespace ) : params = ( namespace , ) execute = self . cursor . execute execute ( 'DELETE FROM gauged_data WHERE namespace = %s' , params ) execute ( 'DELETE FROM gauged_statistics WHERE namespace = %s' , params ) execute ( 'DELETE FROM gauged_keys WHERE namespace = %s' , params ) self . ...
Remove all data associated with the current namespace
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def remove_cache ( self , namespace , key = None ) : if key is None : self . cursor . execute ( 'DELETE FROM gauged_cache ' 'WHERE namespace = %s' , ( namespace , ) ) else : self . cursor . execute ( 'DELETE FROM gauged_cache ' 'WHERE namespace = %s and `key` = %s' , ( namespace , key ) )
Remove all cached values for the specified namespace optionally specifying a key
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def clear_schema ( self ) : execute = self . cursor . execute execute ( 'TRUNCATE TABLE gauged_data' ) execute ( 'TRUNCATE TABLE gauged_keys' ) execute ( 'TRUNCATE TABLE gauged_writer_history' ) execute ( 'TRUNCATE TABLE gauged_cache' ) execute ( 'TRUNCATE TABLE gauged_statistics' ) self . db . commit ( )
Clear all gauged data
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def quantum_random ( ) : import quantumrandom data16 = quantumrandom . uint16 ( array_length = 2 ) assert data16 . flags [ 'C_CONTIGUOUS' ] data32 = data16 . view ( np . dtype ( 'uint32' ) ) [ 0 ] return data32
returns a 32 bit unsigned integer quantum random number
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def _npstate_to_pystate ( npstate ) : PY_VERSION = 3 version , keys , pos , has_gauss , cached_gaussian_ = npstate keys_pos = tuple ( map ( int , keys ) ) + ( int ( pos ) , ) cached_gaussian_ = cached_gaussian_ if has_gauss else None pystate = ( PY_VERSION , keys_pos , cached_gaussian_ ) return pystate
Convert state of a NumPy RandomState object to a state that can be used by Python s Random .
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def _pystate_to_npstate ( pystate ) : NP_VERSION = 'MT19937' version , keys_pos_ , cached_gaussian_ = pystate keys , pos = keys_pos_ [ : - 1 ] , keys_pos_ [ - 1 ] keys = np . array ( keys , dtype = np . uint32 ) has_gauss = cached_gaussian_ is not None cached_gaussian = cached_gaussian_ if has_gauss else 0.0 npstate = ...
Convert state of a Python Random object to state usable by NumPy RandomState .
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def ensure_rng ( rng , impl = 'numpy' ) : if impl == 'numpy' : if rng is None : rng = np . random elif isinstance ( rng , int ) : rng = np . random . RandomState ( seed = rng ) elif isinstance ( rng , random . Random ) : # Convert python to numpy random state py_rng = rng pystate = py_rng . getstate ( ) npstate = _pyst...
Returns a random number generator
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def random_indexes ( max_index , subset_size = None , seed = None , rng = None ) : subst_ = np . arange ( 0 , max_index ) rng = ensure_rng ( seed if rng is None else rng ) rng . shuffle ( subst_ ) if subset_size is None : subst = subst_ else : subst = subst_ [ 0 : min ( subset_size , max_index ) ] return subst
random unrepeated indicies
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