Datasets:
Denis641
/
AdvTestNegatives

Dataset card Data Studio Files
xet
Community
1
query
stringlengths
5
1.23k
positive
stringlengths
53
15.2k
id_
int64
0
252k
task_name
stringlengths
87
242
negative
listlengths
20
553
Parse atom block into atom objects
def atoms ( lines ) : # Convert sdf style charge to actual charge conv_charge_table = { 0 : 0 , 1 : 3 , 2 : 2 , 3 : 1 , 4 : 0 , 5 : - 1 , 6 : - 2 , 7 : - 3 } results = { } for i , line in enumerate ( lines ) : symbol = line [ 31 : 34 ] . rstrip ( ) try : atom = Atom ( symbol ) except KeyError : raise ValueError ( symbol ) xpos = float ( line [ 0 : 10 ] ) ypos = float ( line [ 10 : 20 ] ) zpos = float ( line [ 20 : 30 ] ) atom . coords = ( xpos , ypos , zpos ) atom . mass_diff = int ( line [ 34 : 37 ] ) old_sdf_charge = int ( line [ 37 : 40 ] ) atom . charge = conv_charge_table [ old_sdf_charge ] if old_sdf_charge == 4 : atom . radical = 1 # atom.stereo_flag = int(line[40:43]) # Not used # valence = int(line[46:49]) # if valence: # atom.valence = valence results [ i + 1 ] = { "atom" : atom } return results
11,800
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/v2000reader.py#L71-L100
[ "def", "_adapt_WSDateTime", "(", "dt", ")", ":", "try", ":", "ts", "=", "int", "(", "(", "dt", ".", "replace", "(", "tzinfo", "=", "pytz", ".", "utc", ")", "-", "datetime", "(", "1970", ",", "1", ",", "1", ",", "tzinfo", "=", "pytz", ".", "utc", ")", ")", ".", "total_seconds", "(", ")", ")", "except", "(", "OverflowError", ",", "OSError", ")", ":", "if", "dt", "<", "datetime", ".", "now", "(", ")", ":", "ts", "=", "0", "else", ":", "ts", "=", "2", "**", "63", "-", "1", "return", "ts" ]
Parse bond block into bond objects
def bonds ( lines , atoms ) : # Convert sdf style stereobond (see chem.model.bond.Bond) conv_stereo_table = { 0 : 0 , 1 : 1 , 3 : 3 , 4 : 3 , 6 : 2 } results = { a : { } for a in atoms } for line in lines : bond = Bond ( ) first = int ( line [ 0 : 3 ] ) second = int ( line [ 3 : 6 ] ) if first > second : bond . is_lower_first = 0 order = int ( line [ 6 : 9 ] ) if order < 4 : bond . order = order bond . type = conv_stereo_table [ int ( line [ 9 : 12 ] ) ] results [ first ] [ second ] = { "bond" : bond } results [ second ] [ first ] = { "bond" : bond } return results
11,801
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/v2000reader.py#L103-L124
[ "def", "_adapt_WSDateTime", "(", "dt", ")", ":", "try", ":", "ts", "=", "int", "(", "(", "dt", ".", "replace", "(", "tzinfo", "=", "pytz", ".", "utc", ")", "-", "datetime", "(", "1970", ",", "1", ",", "1", ",", "tzinfo", "=", "pytz", ".", "utc", ")", ")", ".", "total_seconds", "(", ")", ")", "except", "(", "OverflowError", ",", "OSError", ")", ":", "if", "dt", "<", "datetime", ".", "now", "(", ")", ":", "ts", "=", "0", "else", ":", "ts", "=", "2", "**", "63", "-", "1", "return", "ts" ]
Parse properties block
def properties ( lines ) : results = { } for i , line in enumerate ( lines ) : type_ = line [ 3 : 6 ] if type_ not in [ "CHG" , "RAD" , "ISO" ] : continue # Other properties are not supported yet count = int ( line [ 6 : 9 ] ) results [ type_ ] = [ ] for j in range ( count ) : idx = int ( line [ 10 + j * 8 : 13 + j * 8 ] ) val = int ( line [ 14 + j * 8 : 17 + j * 8 ] ) results [ type_ ] . append ( ( idx , val ) ) return results
11,802
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/v2000reader.py#L127-L144
[ "def", "_adapt_WSDateTime", "(", "dt", ")", ":", "try", ":", "ts", "=", "int", "(", "(", "dt", ".", "replace", "(", "tzinfo", "=", "pytz", ".", "utc", ")", "-", "datetime", "(", "1970", ",", "1", ",", "1", ",", "tzinfo", "=", "pytz", ".", "utc", ")", ")", ".", "total_seconds", "(", ")", ")", "except", "(", "OverflowError", ",", "OSError", ")", ":", "if", "dt", "<", "datetime", ".", "now", "(", ")", ":", "ts", "=", "0", "else", ":", "ts", "=", "2", "**", "63", "-", "1", "return", "ts" ]
apply properties to the molecule object
def add_properties ( props , mol ) : if not props : return # The properties supersedes all charge and radical values in the atom block for _ , atom in mol . atoms_iter ( ) : atom . charge = 0 atom . multi = 1 atom . mass = None for prop in props . get ( "CHG" , [ ] ) : mol . atom ( prop [ 0 ] ) . charge = prop [ 1 ] for prop in props . get ( "RAD" , [ ] ) : mol . atom ( prop [ 0 ] ) . multi = prop [ 1 ] for prop in props . get ( "ISO" , [ ] ) : mol . atom ( prop [ 0 ] ) . mass = prop [ 1 ]
11,803
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/v2000reader.py#L147-L165
[ "def", "hurst", "(", "X", ")", ":", "X", "=", "numpy", ".", "array", "(", "X", ")", "N", "=", "X", ".", "size", "T", "=", "numpy", ".", "arange", "(", "1", ",", "N", "+", "1", ")", "Y", "=", "numpy", ".", "cumsum", "(", "X", ")", "Ave_T", "=", "Y", "/", "T", "S_T", "=", "numpy", ".", "zeros", "(", "N", ")", "R_T", "=", "numpy", ".", "zeros", "(", "N", ")", "for", "i", "in", "range", "(", "N", ")", ":", "S_T", "[", "i", "]", "=", "numpy", ".", "std", "(", "X", "[", ":", "i", "+", "1", "]", ")", "X_T", "=", "Y", "-", "T", "*", "Ave_T", "[", "i", "]", "R_T", "[", "i", "]", "=", "numpy", ".", "ptp", "(", "X_T", "[", ":", "i", "+", "1", "]", ")", "R_S", "=", "R_T", "/", "S_T", "R_S", "=", "numpy", ".", "log", "(", "R_S", ")", "[", "1", ":", "]", "n", "=", "numpy", ".", "log", "(", "T", ")", "[", "1", ":", "]", "A", "=", "numpy", ".", "column_stack", "(", "(", "n", ",", "numpy", ".", "ones", "(", "n", ".", "size", ")", ")", ")", "[", "m", ",", "c", "]", "=", "numpy", ".", "linalg", ".", "lstsq", "(", "A", ",", "R_S", ")", "[", "0", "]", "H", "=", "m", "return", "H" ]
Parse molfile part into molecule object
def molecule ( lines ) : count_line = lines [ 3 ] num_atoms = int ( count_line [ 0 : 3 ] ) num_bonds = int ( count_line [ 3 : 6 ] ) # chiral_flag = int(count_line[12:15]) # Not used # num_prop = int(count_line[30:33]) # "No longer supported" compound = Compound ( ) compound . graph . _node = atoms ( lines [ 4 : num_atoms + 4 ] ) compound . graph . _adj = bonds ( lines [ num_atoms + 4 : num_atoms + num_bonds + 4 ] , compound . graph . _node . keys ( ) ) props = properties ( lines [ num_atoms + num_bonds + 4 : ] ) add_properties ( props , compound ) return compound
11,804
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/v2000reader.py#L168-L189
[ "def", "hurst", "(", "X", ")", ":", "X", "=", "numpy", ".", "array", "(", "X", ")", "N", "=", "X", ".", "size", "T", "=", "numpy", ".", "arange", "(", "1", ",", "N", "+", "1", ")", "Y", "=", "numpy", ".", "cumsum", "(", "X", ")", "Ave_T", "=", "Y", "/", "T", "S_T", "=", "numpy", ".", "zeros", "(", "N", ")", "R_T", "=", "numpy", ".", "zeros", "(", "N", ")", "for", "i", "in", "range", "(", "N", ")", ":", "S_T", "[", "i", "]", "=", "numpy", ".", "std", "(", "X", "[", ":", "i", "+", "1", "]", ")", "X_T", "=", "Y", "-", "T", "*", "Ave_T", "[", "i", "]", "R_T", "[", "i", "]", "=", "numpy", ".", "ptp", "(", "X_T", "[", ":", "i", "+", "1", "]", ")", "R_S", "=", "R_T", "/", "S_T", "R_S", "=", "numpy", ".", "log", "(", "R_S", ")", "[", "1", ":", "]", "n", "=", "numpy", ".", "log", "(", "T", ")", "[", "1", ":", "]", "A", "=", "numpy", ".", "column_stack", "(", "(", "n", ",", "numpy", ".", "ones", "(", "n", ".", "size", ")", ")", ")", "[", "m", ",", "c", "]", "=", "numpy", ".", "linalg", ".", "lstsq", "(", "A", ",", "R_S", ")", "[", "0", "]", "H", "=", "m", "return", "H" ]
Yields molecules generated from CTAB text
def mol_supplier ( lines , no_halt , assign_descriptors ) : def sdf_block ( lns ) : mol = [ ] opt = [ ] is_mol = True for line in lns : if line . startswith ( "$$$$" ) : yield mol [ : ] , opt [ : ] is_mol = True mol . clear ( ) opt . clear ( ) elif line . startswith ( "M END" ) : is_mol = False elif is_mol : mol . append ( line . rstrip ( ) ) else : opt . append ( line . rstrip ( ) ) if mol : yield mol , opt for i , ( mol , opt ) in enumerate ( sdf_block ( lines ) ) : try : c = molecule ( mol ) if assign_descriptors : molutil . assign_descriptors ( c ) except ValueError as err : if no_halt : print ( "Unsupported symbol: {} (#{} in v2000reader)" . format ( err , i + 1 ) ) c = molutil . null_molecule ( assign_descriptors ) else : raise ValueError ( "Unsupported symbol: {}" . format ( err ) ) except RuntimeError as err : if no_halt : print ( "Failed to minimize ring: {} (#{} in v2000reader)" . format ( err , i + 1 ) ) else : raise RuntimeError ( "Failed to minimize ring: {}" . format ( err ) ) except : if no_halt : print ( "Unexpected error (#{} in v2000reader)" . format ( i + 1 ) ) c = molutil . null_molecule ( assign_descriptors ) c . data = optional_data ( opt ) yield c continue else : print ( traceback . format_exc ( ) ) raise Exception ( "Unsupported Error" ) c . data = optional_data ( opt ) yield c
11,805
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/v2000reader.py#L192-L253
[ "def", "get_valid_times_for_job_legacy", "(", "self", ",", "num_job", ")", ":", "# All of this should be integers, so no rounding factors needed.", "shift_dur", "=", "self", ".", "curr_seg", "[", "0", "]", "+", "int", "(", "self", ".", "job_time_shift", "*", "num_job", ")", "job_valid_seg", "=", "self", ".", "valid_chunk", ".", "shift", "(", "shift_dur", ")", "# If this is the last job, push the end back", "if", "num_job", "==", "(", "self", ".", "num_jobs", "-", "1", ")", ":", "dataPushBack", "=", "self", ".", "data_length", "-", "self", ".", "valid_chunk", "[", "1", "]", "job_valid_seg", "=", "segments", ".", "segment", "(", "job_valid_seg", "[", "0", "]", ",", "self", ".", "curr_seg", "[", "1", "]", "-", "dataPushBack", ")", "return", "job_valid_seg" ]
Returns molecules generated from sdfile text
def mols_from_text ( text , no_halt = True , assign_descriptors = True ) : if isinstance ( text , bytes ) : t = tx . decode ( text ) else : t = text # Lazy line splitter. More efficient memory usage than str.split. exp = re . compile ( r"[^\n]*\n|." ) sp = ( x . group ( 0 ) for x in re . finditer ( exp , t ) ) for c in mol_supplier ( sp , no_halt , assign_descriptors ) : yield c
11,806
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/v2000reader.py#L256-L271
[ "def", "find_best_candidate", "(", "self", ")", ":", "self", ".", "fill_percent_done", "(", ")", "i_b", "=", "np", ".", "argmax", "(", "self", ".", "percent_done", ".", "ravel", "(", ")", ")", "if", "self", ".", "percent_done", ".", "ravel", "(", ")", "[", "i_b", "]", "<=", "0", ":", "return", "None", "# check for ties", "I", "=", "self", ".", "percent_done", ".", "ravel", "(", ")", "==", "self", ".", "percent_done", ".", "ravel", "(", ")", "[", "i_b", "]", "if", "I", ".", "sum", "(", ")", "==", "1", ":", "return", "i_b", "else", ":", "I2", "=", "np", ".", "argmax", "(", "self", ".", "max_elev", ".", "ravel", "(", ")", "[", "I", "]", ")", "return", "I", ".", "nonzero", "(", ")", "[", "0", "]", "[", "I2", "]" ]
Parse CTAB text and return first one as a Compound object .
def mol_from_text ( text , assign_descriptors = True ) : cg = mols_from_text ( text , False , assign_descriptors ) return next ( cg )
11,807
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/v2000reader.py#L274-L282
[ "def", "streaming_init", "(", "self", ")", ":", "system", "=", "self", ".", "system", "config", "=", "self", ".", "config", "if", "system", ".", "config", ".", "dime_enable", ":", "config", ".", "compute_flows", "=", "True", "system", ".", "streaming", ".", "send_init", "(", "recepient", "=", "'all'", ")", "logger", ".", "info", "(", "'Waiting for modules to send init info...'", ")", "sleep", "(", "0.5", ")", "system", ".", "streaming", ".", "sync_and_handle", "(", ")" ]
Parse CTAB file and return first one as a Compound object .
def mol_from_file ( path , assign_descriptors = True ) : cs = mols_from_file ( path , False , assign_descriptors ) return next ( cs )
11,808
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/v2000reader.py#L293-L296
[ "def", "perturbParams", "(", "self", ",", "pertSize", "=", "1e-3", ")", ":", "params", "=", "self", ".", "getParams", "(", ")", "self", ".", "setParams", "(", "params", "+", "pertSize", "*", "sp", ".", "randn", "(", "params", ".", "shape", "[", "0", "]", ")", ")" ]
Returns the contents of a file resource .
def load_from_resource ( name ) : filepath = Path ( USER_DIR ) / name if filepath . exists ( ) : with filepath . open ( ) as fh : return fh . read ( ) else : return resource_string ( 'wdiffhtml' , 'data/' + name ) . decode ( 'utf-8' )
11,809
https://github.com/brutus/wdiffhtml/blob/e97b524a7945f7a626e33ec141343120c524d9fa/wdiffhtml/settings.py#L40-L53
[ "def", "clearAndSetComboBoxes", "(", "self", ",", "axesNames", ")", ":", "logger", ".", "debug", "(", "\"Collector clearAndSetComboBoxes: {}\"", ".", "format", "(", "axesNames", ")", ")", "check_is_a_sequence", "(", "axesNames", ")", "row", "=", "0", "self", ".", "_deleteComboBoxes", "(", "row", ")", "self", ".", "clear", "(", ")", "self", ".", "_setAxesNames", "(", "axesNames", ")", "self", ".", "_createComboBoxes", "(", "row", ")", "self", ".", "_updateWidgets", "(", ")" ]
Creates a new connection to the Slack Real - Time API .
def connect ( token , protocol = RtmProtocol , factory = WebSocketClientFactory , factory_kwargs = None , api_url = None , debug = False ) : if factory_kwargs is None : factory_kwargs = dict ( ) metadata = request_session ( token , api_url ) wsfactory = factory ( metadata . url , * * factory_kwargs ) if debug : warnings . warn ( 'debug=True has been deprecated in autobahn 0.14.0' ) wsfactory . protocol = lambda * a , * * k : protocol ( * a , * * k ) . _seedMetadata ( metadata ) connection = connectWS ( wsfactory ) return connection
11,810
https://github.com/micolous/python-slackrealtime/blob/e9c94416f979a6582110ebba09c147de2bfe20a1/src/slackrealtime/__init__.py#L26-L43
[ "def", "match_ancestor_bank_id", "(", "self", ",", "bank_id", ",", "match", ")", ":", "# matches when the bank_id param is an ancestor of", "# any bank", "bank_descendants", "=", "self", ".", "_get_descendant_catalog_ids", "(", "bank_id", ")", "identifiers", "=", "[", "ObjectId", "(", "i", ".", "identifier", ")", "for", "i", "in", "bank_descendants", "]", "self", ".", "_query_terms", "[", "'_id'", "]", "=", "{", "'$in'", ":", "identifiers", "}" ]
This could probably be improved ; at the moment it starts by trying to overshoot the desired compressed block size then it reduces the input bytes one by one until it has met the required block size
def next_block ( self ) : assert self . pos <= self . input_len if self . pos == self . input_len : return None # Overshoot i = self . START_OVERSHOOT while True : try_size = int ( self . bs * i ) size = self . check_request_size ( try_size ) c , d = self . compress_next_chunk ( size ) if size != try_size : break if len ( d ) < self . bs : i += self . OVERSHOOT_INCREASE else : break # Reduce by one byte until we hit the target while True : if len ( d ) <= self . bs : self . c = c # self.c = self.factory() crc32 = zlib . crc32 ( self . get_input ( size ) , 0xffffffff ) & 0xffffffff self . pos += size self . compressed_bytes += len ( d ) return crc32 , size , d size -= 1 if size == 0 : return None c , d = self . compress_next_chunk ( size )
11,811
https://github.com/xlfe/reticul8/blob/0f9503f7a0731ae09adfe4c9af9b57327a7f9d84/python/reticul8/block_compressor.py#L57-L101
[ "def", "_SeparateTypes", "(", "self", ",", "metadata_value_pairs", ")", ":", "registry_pairs", "=", "[", "]", "file_pairs", "=", "[", "]", "match_pairs", "=", "[", "]", "for", "metadata", ",", "result", "in", "metadata_value_pairs", ":", "if", "(", "result", ".", "stat_entry", ".", "pathspec", ".", "pathtype", "==", "rdf_paths", ".", "PathSpec", ".", "PathType", ".", "REGISTRY", ")", ":", "registry_pairs", ".", "append", "(", "(", "metadata", ",", "result", ".", "stat_entry", ")", ")", "else", ":", "file_pairs", ".", "append", "(", "(", "metadata", ",", "result", ")", ")", "match_pairs", ".", "extend", "(", "[", "(", "metadata", ",", "match", ")", "for", "match", "in", "result", ".", "matches", "]", ")", "return", "registry_pairs", ",", "file_pairs", ",", "match_pairs" ]
Configure logging settings and return a logger object .
def set_up_logging ( log_file , console_log_level ) : logger = logging . getLogger ( ) logger . setLevel ( logging . DEBUG ) fh = logging . FileHandler ( str ( log_file ) ) fh . setLevel ( logging . DEBUG ) ch = logging . StreamHandler ( ) ch . setLevel ( console_log_level ) formatter = logging . Formatter ( "{asctime} {levelname} ({name}): {message}" , style = '{' ) fh . setFormatter ( formatter ) ch . setFormatter ( formatter ) logger . addHandler ( fh ) logger . addHandler ( ch ) return logger
11,812
https://github.com/mesbahamin/chronophore/blob/ee140c61b4dfada966f078de8304bac737cec6f7/chronophore/chronophore.py#L48-L64
[ "def", "trust_notebook", "(", "self", ",", "path", ")", ":", "if", "path", ".", "endswith", "(", "'.ipynb'", ")", "or", "path", "not", "in", "self", ".", "paired_notebooks", ":", "super", "(", "TextFileContentsManager", ",", "self", ")", ".", "trust_notebook", "(", "path", ")", "return", "fmt", ",", "formats", "=", "self", ".", "paired_notebooks", "[", "path", "]", "for", "alt_path", ",", "alt_fmt", "in", "paired_paths", "(", "path", ",", "fmt", ",", "formats", ")", ":", "if", "alt_fmt", "[", "'extension'", "]", "==", "'.ipynb'", ":", "super", "(", "TextFileContentsManager", ",", "self", ")", ".", "trust_notebook", "(", "alt_path", ")" ]
Run Chronophore based on the command line arguments .
def main ( ) : args = get_args ( ) # Make Chronophore's directories and files in $HOME DATA_DIR = pathlib . Path ( appdirs . user_data_dir ( __title__ ) ) LOG_FILE = pathlib . Path ( appdirs . user_log_dir ( __title__ ) , 'debug.log' ) os . makedirs ( str ( DATA_DIR ) , exist_ok = True ) os . makedirs ( str ( LOG_FILE . parent ) , exist_ok = True ) if args . version : print ( '{} {}' . format ( __title__ , __version__ ) ) raise SystemExit if args . debug : CONSOLE_LOG_LEVEL = logging . DEBUG elif args . verbose : CONSOLE_LOG_LEVEL = logging . INFO else : CONSOLE_LOG_LEVEL = logging . WARNING logger = set_up_logging ( LOG_FILE , CONSOLE_LOG_LEVEL ) logger . debug ( '-' * 80 ) logger . info ( '{} {}' . format ( __title__ , __version__ ) ) logger . debug ( 'Log File: {}' . format ( LOG_FILE ) ) logger . debug ( 'Data Directory: {}' . format ( DATA_DIR ) ) if args . testdb : DATABASE_FILE = DATA_DIR . joinpath ( 'test.sqlite' ) logger . info ( 'Using test database.' ) else : DATABASE_FILE = DATA_DIR . joinpath ( 'chronophore.sqlite' ) logger . debug ( 'Database File: {}' . format ( DATABASE_FILE ) ) engine = create_engine ( 'sqlite:///{}' . format ( str ( DATABASE_FILE ) ) ) Base . metadata . create_all ( engine ) Session . configure ( bind = engine ) if args . log_sql : logging . getLogger ( 'sqlalchemy.engine' ) . setLevel ( logging . INFO ) if args . testdb : add_test_users ( session = Session ( ) ) controller . flag_forgotten_entries ( session = Session ( ) ) if args . tk : from chronophore . tkview import TkChronophoreUI TkChronophoreUI ( ) else : try : from PyQt5 . QtWidgets import QApplication except ImportError : print ( 'Error: PyQt5, which chronophore uses for its' + ' graphical interface, is not installed.' + "\nInstall it with 'pip install PyQt5'" + " or use the old Tk ui with 'chronophore --tk'." ) raise SystemExit else : from chronophore . qtview import QtChronophoreUI app = QApplication ( sys . argv ) chrono_ui = QtChronophoreUI ( ) chrono_ui . show ( ) sys . exit ( app . exec_ ( ) ) logger . debug ( '{} stopping' . format ( __title__ ) )
11,813
https://github.com/mesbahamin/chronophore/blob/ee140c61b4dfada966f078de8304bac737cec6f7/chronophore/chronophore.py#L67-L134
[ "def", "init_conv_weight", "(", "layer", ")", ":", "n_filters", "=", "layer", ".", "filters", "filter_shape", "=", "(", "layer", ".", "kernel_size", ",", ")", "*", "get_n_dim", "(", "layer", ")", "weight", "=", "np", ".", "zeros", "(", "(", "n_filters", ",", "n_filters", ")", "+", "filter_shape", ")", "center", "=", "tuple", "(", "map", "(", "lambda", "x", ":", "int", "(", "(", "x", "-", "1", ")", "/", "2", ")", ",", "filter_shape", ")", ")", "for", "i", "in", "range", "(", "n_filters", ")", ":", "filter_weight", "=", "np", ".", "zeros", "(", "(", "n_filters", ",", ")", "+", "filter_shape", ")", "index", "=", "(", "i", ",", ")", "+", "center", "filter_weight", "[", "index", "]", "=", "1", "weight", "[", "i", ",", "...", "]", "=", "filter_weight", "bias", "=", "np", ".", "zeros", "(", "n_filters", ")", "layer", ".", "set_weights", "(", "(", "add_noise", "(", "weight", ",", "np", ".", "array", "(", "[", "0", ",", "1", "]", ")", ")", ",", "add_noise", "(", "bias", ",", "np", ".", "array", "(", "[", "0", ",", "1", "]", ")", ")", ")", ")" ]
Determines if the record should be logged and injects context info into the record . Always returns True
def filter ( self , record ) : fmt = LogManager . spec . context_format if fmt : data = self . context . to_dict ( ) if data : record . context = fmt % "," . join ( "%s=%s" % ( key , val ) for key , val in sorted ( data . items ( ) ) if key and val ) else : record . context = "" return True
11,814
https://github.com/zsimic/runez/blob/14363b719a1aae1528859a501a22d075ce0abfcc/src/runez/logsetup.py#L142-L151
[ "def", "reset", "(", "self", ")", ":", "for", "alternative", "in", "self", ".", "alternatives", ":", "alternative", ".", "reset", "(", ")", "self", ".", "reset_winner", "(", ")", "self", ".", "increment_version", "(", ")" ]
Enable dumping thread stack traces when specified signals are received similar to java s handling of SIGQUIT
def enable_faulthandler ( cls , signum = signal . SIGUSR1 ) : with cls . _lock : if not signum : cls . _disable_faulthandler ( ) return if not cls . file_handler or faulthandler is None : return cls . faulthandler_signum = signum dump_file = cls . file_handler . stream faulthandler . enable ( file = dump_file , all_threads = True ) faulthandler . register ( signum , file = dump_file , all_threads = True , chain = False )
11,815
https://github.com/zsimic/runez/blob/14363b719a1aae1528859a501a22d075ce0abfcc/src/runez/logsetup.py#L383-L401
[ "async", "def", "update_lease_async", "(", "self", ",", "lease", ")", ":", "if", "lease", "is", "None", ":", "return", "False", "if", "not", "lease", ".", "token", ":", "return", "False", "_logger", ".", "debug", "(", "\"Updating lease %r %r\"", ",", "self", ".", "host", ".", "guid", ",", "lease", ".", "partition_id", ")", "# First, renew the lease to make sure the update will go through.", "if", "await", "self", ".", "renew_lease_async", "(", "lease", ")", ":", "try", ":", "await", "self", ".", "host", ".", "loop", ".", "run_in_executor", "(", "self", ".", "executor", ",", "functools", ".", "partial", "(", "self", ".", "storage_client", ".", "create_blob_from_text", ",", "self", ".", "lease_container_name", ",", "lease", ".", "partition_id", ",", "json", ".", "dumps", "(", "lease", ".", "serializable", "(", ")", ")", ",", "lease_id", "=", "lease", ".", "token", ")", ")", "except", "Exception", "as", "err", ":", "# pylint: disable=broad-except", "_logger", ".", "error", "(", "\"Failed to update lease %r %r %r\"", ",", "self", ".", "host", ".", "guid", ",", "lease", ".", "partition_id", ",", "err", ")", "raise", "err", "else", ":", "return", "False", "return", "True" ]
OVerride spec and _default_spec with given values
def override_spec ( cls , * * kwargs ) : cls . _default_spec . set ( * * kwargs ) cls . spec . set ( * * kwargs )
11,816
https://github.com/zsimic/runez/blob/14363b719a1aae1528859a501a22d075ce0abfcc/src/runez/logsetup.py#L404-L407
[ "def", "_index_audio_cmu", "(", "self", ",", "basename", "=", "None", ",", "replace_already_indexed", "=", "False", ")", ":", "self", ".", "_prepare_audio", "(", "basename", "=", "basename", ",", "replace_already_indexed", "=", "replace_already_indexed", ")", "for", "staging_audio_basename", "in", "self", ".", "_list_audio_files", "(", "sub_dir", "=", "\"staging\"", ")", ":", "original_audio_name", "=", "''", ".", "join", "(", "staging_audio_basename", ".", "split", "(", "'.'", ")", "[", ":", "-", "1", "]", ")", "[", ":", "-", "3", "]", "pocketsphinx_command", "=", "''", ".", "join", "(", "[", "\"pocketsphinx_continuous\"", ",", "\"-infile\"", ",", "str", "(", "\"{}/staging/{}\"", ".", "format", "(", "self", ".", "src_dir", ",", "staging_audio_basename", ")", ")", ",", "\"-time\"", ",", "\"yes\"", ",", "\"-logfn\"", ",", "\"/dev/null\"", "]", ")", "try", ":", "if", "self", ".", "get_verbosity", "(", ")", ":", "print", "(", "\"Now indexing {}\"", ".", "format", "(", "staging_audio_basename", ")", ")", "output", "=", "subprocess", ".", "check_output", "(", "[", "\"pocketsphinx_continuous\"", ",", "\"-infile\"", ",", "str", "(", "\"{}/staging/{}\"", ".", "format", "(", "self", ".", "src_dir", ",", "staging_audio_basename", ")", ")", ",", "\"-time\"", ",", "\"yes\"", ",", "\"-logfn\"", ",", "\"/dev/null\"", "]", ",", "universal_newlines", "=", "True", ")", ".", "split", "(", "'\\n'", ")", "str_timestamps_with_sil_conf", "=", "list", "(", "map", "(", "lambda", "x", ":", "x", ".", "split", "(", "\" \"", ")", ",", "filter", "(", "None", ",", "output", "[", "1", ":", "]", ")", ")", ")", "# Timestamps are putted in a list of a single element. To match", "# Watson's output.", "self", ".", "__timestamps_unregulated", "[", "original_audio_name", "+", "\".wav\"", "]", "=", "[", "(", "self", ".", "_timestamp_extractor_cmu", "(", "staging_audio_basename", ",", "str_timestamps_with_sil_conf", ")", ")", "]", "if", "self", ".", "get_verbosity", "(", ")", ":", "print", "(", "\"Done indexing {}\"", ".", "format", "(", "staging_audio_basename", ")", ")", "except", "OSError", "as", "e", ":", "if", "self", ".", "get_verbosity", "(", ")", ":", "print", "(", "e", ",", "\"The command was: {}\"", ".", "format", "(", "pocketsphinx_command", ")", ")", "self", ".", "__errors", "[", "(", "time", "(", ")", ",", "staging_audio_basename", ")", "]", "=", "e", "self", ".", "_timestamp_regulator", "(", ")", "if", "self", ".", "get_verbosity", "(", ")", ":", "print", "(", "\"Finished indexing procedure\"", ")" ]
Fix standard logging shortcuts to correctly report logging module .
def _fix_logging_shortcuts ( cls ) : if cls . is_using_format ( "%(pathname)s %(filename)s %(funcName)s %(module)s" ) : logging . _srcfile = cls . _logging_snapshot . _srcfile else : logging . _srcfile = None logging . logProcesses = cls . is_using_format ( "%(process)d" ) logging . logThreads = cls . is_using_format ( "%(thread)d %(threadName)s" ) def getframe ( ) : return sys . _getframe ( 4 ) def log ( level , msg , * args , * * kwargs ) : """Wrapper to make logging.info() etc report the right module %(name)""" name = get_caller_name ( ) logger = logging . getLogger ( name ) try : logging . currentframe = getframe logger . log ( level , msg , * args , * * kwargs ) finally : logging . currentframe = ORIGINAL_CF def wrap ( level , * * kwargs ) : """Wrap corresponding logging shortcut function""" original = getattr ( logging , logging . getLevelName ( level ) . lower ( ) ) f = partial ( log , level , * * kwargs ) f . __doc__ = original . __doc__ return f logging . critical = wrap ( logging . CRITICAL ) logging . fatal = logging . critical logging . error = wrap ( logging . ERROR ) logging . exception = partial ( logging . error , exc_info = True ) logging . warning = wrap ( logging . WARNING ) logging . info = wrap ( logging . INFO ) logging . debug = wrap ( logging . DEBUG ) logging . log = log
11,817
https://github.com/zsimic/runez/blob/14363b719a1aae1528859a501a22d075ce0abfcc/src/runez/logsetup.py#L439-L491
[ "def", "fileupdate", "(", "self", ",", "data", ")", ":", "self", ".", "name", "=", "data", "[", "\"name\"", "]", "add", "=", "self", ".", "__additional", "add", "[", "\"filetype\"", "]", "=", "\"other\"", "for", "filetype", "in", "(", "\"book\"", ",", "\"image\"", ",", "\"video\"", ",", "\"audio\"", ",", "\"archive\"", ")", ":", "if", "filetype", "in", "data", ":", "add", "[", "\"filetype\"", "]", "=", "filetype", "break", "if", "add", "[", "\"filetype\"", "]", "in", "(", "\"image\"", ",", "\"video\"", ",", "\"audio\"", ")", ":", "add", "[", "\"thumb\"", "]", "=", "data", ".", "get", "(", "\"thumb\"", ",", "dict", "(", ")", ")", "# checksum is md5", "add", "[", "\"checksum\"", "]", "=", "data", "[", "\"checksum\"", "]", "add", "[", "\"expire_time\"", "]", "=", "data", "[", "\"expires\"", "]", "/", "1000", "add", "[", "\"size\"", "]", "=", "data", "[", "\"size\"", "]", "add", "[", "\"info\"", "]", "=", "data", ".", "get", "(", "add", "[", "\"filetype\"", "]", ",", "dict", "(", ")", ")", "add", "[", "\"uploader\"", "]", "=", "data", "[", "\"user\"", "]", "if", "self", ".", "room", ".", "admin", ":", "add", "[", "\"info\"", "]", ".", "update", "(", "{", "\"room\"", ":", "data", ".", "get", "(", "\"room\"", ")", "}", ")", "add", "[", "\"info\"", "]", ".", "update", "(", "{", "\"uploader_ip\"", ":", "data", ".", "get", "(", "\"uploader_ip\"", ")", "}", ")", "self", ".", "updated", "=", "True" ]
A hack to get the content of the XML responses from the CAS server .
def _parse_single ( self , text , tagname ) : return minidom . parseString ( text ) . getElementsByTagName ( tagname ) [ 0 ] . firstChild . data
11,818
https://github.com/dfm/casjobs/blob/1cc3f5511cc254d776082909221787e3c037ac16/casjobs.py#L93-L108
[ "def", "use_defaults", "(", "func", ")", ":", "@", "wraps", "(", "func", ")", "def", "wrapper", "(", "row", ",", "cohort", ",", "filter_fn", "=", "None", ",", "normalized_per_mb", "=", "None", ",", "*", "*", "kwargs", ")", ":", "filter_fn", "=", "first_not_none_param", "(", "[", "filter_fn", ",", "cohort", ".", "filter_fn", "]", ",", "no_filter", ")", "normalized_per_mb", "=", "first_not_none_param", "(", "[", "normalized_per_mb", ",", "cohort", ".", "normalized_per_mb", "]", ",", "False", ")", "return", "func", "(", "row", "=", "row", ",", "cohort", "=", "cohort", ",", "filter_fn", "=", "filter_fn", ",", "normalized_per_mb", "=", "normalized_per_mb", ",", "*", "*", "kwargs", ")", "return", "wrapper" ]
Run a quick job .
def quick ( self , q , context = None , task_name = "quickie" , system = False ) : if not context : context = self . context params = { "qry" : q , "context" : context , "taskname" : task_name , "isSystem" : system } r = self . _send_request ( "ExecuteQuickJob" , params = params ) return self . _parse_single ( r . text , "string" )
11,819
https://github.com/dfm/casjobs/blob/1cc3f5511cc254d776082909221787e3c037ac16/casjobs.py#L110-L135
[ "def", "destroy_sns_event", "(", "app_name", ",", "env", ",", "region", ")", ":", "session", "=", "boto3", ".", "Session", "(", "profile_name", "=", "env", ",", "region_name", "=", "region", ")", "sns_client", "=", "session", ".", "client", "(", "'sns'", ")", "lambda_subscriptions", "=", "get_sns_subscriptions", "(", "app_name", "=", "app_name", ",", "env", "=", "env", ",", "region", "=", "region", ")", "for", "subscription_arn", "in", "lambda_subscriptions", ":", "sns_client", ".", "unsubscribe", "(", "SubscriptionArn", "=", "subscription_arn", ")", "LOG", ".", "debug", "(", "\"Lambda SNS event deleted\"", ")", "return", "True" ]
Submit a job to CasJobs .
def submit ( self , q , context = None , task_name = "casjobs" , estimate = 30 ) : if not context : context = self . context params = { "qry" : q , "context" : context , "taskname" : task_name , "estimate" : estimate } r = self . _send_request ( "SubmitJob" , params = params ) job_id = int ( self . _parse_single ( r . text , "long" ) ) return job_id
11,820
https://github.com/dfm/casjobs/blob/1cc3f5511cc254d776082909221787e3c037ac16/casjobs.py#L137-L162
[ "def", "from_string", "(", "contents", ")", ":", "if", "contents", "[", "-", "1", "]", "!=", "\"\\n\"", ":", "contents", "+=", "\"\\n\"", "white_space", "=", "r\"[ \\t\\r\\f\\v]\"", "natoms_line", "=", "white_space", "+", "r\"*\\d+\"", "+", "white_space", "+", "r\"*\\n\"", "comment_line", "=", "r\"[^\\n]*\\n\"", "coord_lines", "=", "r\"(\\s*\\w+\\s+[0-9\\-\\+\\.eEdD]+\\s+[0-9\\-\\+\\.eEdD]+\\s+[0-9\\-\\+\\.eEdD]+\\s*\\n)+\"", "frame_pattern_text", "=", "natoms_line", "+", "comment_line", "+", "coord_lines", "pat", "=", "re", ".", "compile", "(", "frame_pattern_text", ",", "re", ".", "MULTILINE", ")", "mols", "=", "[", "]", "for", "xyz_match", "in", "pat", ".", "finditer", "(", "contents", ")", ":", "xyz_text", "=", "xyz_match", ".", "group", "(", "0", ")", "mols", ".", "append", "(", "XYZ", ".", "_from_frame_string", "(", "xyz_text", ")", ")", "return", "XYZ", "(", "mols", ")" ]
Check the status of a job .
def status ( self , job_id ) : params = { "jobid" : job_id } r = self . _send_request ( "GetJobStatus" , params = params ) status = int ( self . _parse_single ( r . text , "int" ) ) return status , self . status_codes [ status ]
11,821
https://github.com/dfm/casjobs/blob/1cc3f5511cc254d776082909221787e3c037ac16/casjobs.py#L164-L181
[ "def", "removefromreadergroup", "(", "self", ",", "groupname", ")", ":", "hresult", ",", "hcontext", "=", "SCardEstablishContext", "(", "SCARD_SCOPE_USER", ")", "if", "0", "!=", "hresult", ":", "raise", "EstablishContextException", "(", "hresult", ")", "try", ":", "hresult", "=", "SCardRemoveReaderFromGroup", "(", "hcontext", ",", "self", ".", "name", ",", "groupname", ")", "if", "0", "!=", "hresult", ":", "raise", "RemoveReaderFromGroupException", "(", "hresult", ",", "self", ".", "name", ",", "groupname", ")", "finally", ":", "hresult", "=", "SCardReleaseContext", "(", "hcontext", ")", "if", "0", "!=", "hresult", ":", "raise", "ReleaseContextException", "(", "hresult", ")" ]
Monitor the status of a job .
def monitor ( self , job_id , timeout = 5 ) : while True : status = self . status ( job_id ) logging . info ( "Monitoring job: %d - Status: %d, %s" % ( job_id , status [ 0 ] , status [ 1 ] ) ) if status [ 0 ] in [ 3 , 4 , 5 ] : return status time . sleep ( timeout )
11,822
https://github.com/dfm/casjobs/blob/1cc3f5511cc254d776082909221787e3c037ac16/casjobs.py#L195-L216
[ "def", "removefromreadergroup", "(", "self", ",", "groupname", ")", ":", "hresult", ",", "hcontext", "=", "SCardEstablishContext", "(", "SCARD_SCOPE_USER", ")", "if", "0", "!=", "hresult", ":", "raise", "EstablishContextException", "(", "hresult", ")", "try", ":", "hresult", "=", "SCardRemoveReaderFromGroup", "(", "hcontext", ",", "self", ".", "name", ",", "groupname", ")", "if", "0", "!=", "hresult", ":", "raise", "RemoveReaderFromGroupException", "(", "hresult", ",", "self", ".", "name", ",", "groupname", ")", "finally", ":", "hresult", "=", "SCardReleaseContext", "(", "hcontext", ")", "if", "0", "!=", "hresult", ":", "raise", "ReleaseContextException", "(", "hresult", ")" ]
Request the output for a given table .
def request_output ( self , table , outtype ) : job_types = [ "CSV" , "DataSet" , "FITS" , "VOTable" ] assert outtype in job_types params = { "tableName" : table , "type" : outtype } r = self . _send_request ( "SubmitExtractJob" , params = params ) job_id = int ( self . _parse_single ( r . text , "long" ) ) return job_id
11,823
https://github.com/dfm/casjobs/blob/1cc3f5511cc254d776082909221787e3c037ac16/casjobs.py#L238-L257
[ "def", "get_license_assignment_manager", "(", "service_instance", ")", ":", "log", ".", "debug", "(", "'Retrieving license assignment manager'", ")", "try", ":", "lic_assignment_manager", "=", "service_instance", ".", "content", ".", "licenseManager", ".", "licenseAssignmentManager", "except", "vim", ".", "fault", ".", "NoPermission", "as", "exc", ":", "log", ".", "exception", "(", "exc", ")", "raise", "salt", ".", "exceptions", ".", "VMwareApiError", "(", "'Not enough permissions. Required privilege: '", "'{0}'", ".", "format", "(", "exc", ".", "privilegeId", ")", ")", "except", "vim", ".", "fault", ".", "VimFault", "as", "exc", ":", "log", ".", "exception", "(", "exc", ")", "raise", "salt", ".", "exceptions", ".", "VMwareApiError", "(", "exc", ".", "msg", ")", "except", "vmodl", ".", "RuntimeFault", "as", "exc", ":", "log", ".", "exception", "(", "exc", ")", "raise", "salt", ".", "exceptions", ".", "VMwareRuntimeError", "(", "exc", ".", "msg", ")", "if", "not", "lic_assignment_manager", ":", "raise", "salt", ".", "exceptions", ".", "VMwareObjectRetrievalError", "(", "'License assignment manager was not retrieved'", ")", "return", "lic_assignment_manager" ]
Download an output file given the id of the output request job .
def get_output ( self , job_id , outfn ) : job_info = self . job_info ( jobid = job_id ) [ 0 ] # Make sure that the job is finished. status = int ( job_info [ "Status" ] ) if status != 5 : raise Exception ( "The status of job %d is %d (%s)" % ( job_id , status , self . status_codes [ status ] ) ) # Try to download the output file. remotefn = job_info [ "OutputLoc" ] r = requests . get ( remotefn ) # Make sure that the request went through. code = r . status_code if code != 200 : raise Exception ( "Getting file %s yielded status: %d" % ( remotefn , code ) ) # Save the data to a file. try : outfn . write ( r . content ) except AttributeError : f = open ( outfn , "wb" ) f . write ( r . content ) f . close ( )
11,824
https://github.com/dfm/casjobs/blob/1cc3f5511cc254d776082909221787e3c037ac16/casjobs.py#L259-L294
[ "def", "secret_file", "(", "filename", ")", ":", "filestat", "=", "os", ".", "stat", "(", "abspath", "(", "filename", ")", ")", "if", "stat", ".", "S_ISREG", "(", "filestat", ".", "st_mode", ")", "==", "0", "and", "stat", ".", "S_ISLNK", "(", "filestat", ".", "st_mode", ")", "==", "0", ":", "e_msg", "=", "\"Secret file %s must be a real file or symlink\"", "%", "filename", "raise", "aomi", ".", "exceptions", ".", "AomiFile", "(", "e_msg", ")", "if", "platform", ".", "system", "(", ")", "!=", "\"Windows\"", ":", "if", "filestat", ".", "st_mode", "&", "stat", ".", "S_IROTH", "or", "filestat", ".", "st_mode", "&", "stat", ".", "S_IWOTH", "or", "filestat", ".", "st_mode", "&", "stat", ".", "S_IWGRP", ":", "e_msg", "=", "\"Secret file %s has too loose permissions\"", "%", "filename", "raise", "aomi", ".", "exceptions", ".", "AomiFile", "(", "e_msg", ")" ]
Shorthand for requesting an output file and then downloading it when ready .
def request_and_get_output ( self , table , outtype , outfn ) : job_id = self . request_output ( table , outtype ) status = self . monitor ( job_id ) if status [ 0 ] != 5 : raise Exception ( "Output request failed." ) self . get_output ( job_id , outfn )
11,825
https://github.com/dfm/casjobs/blob/1cc3f5511cc254d776082909221787e3c037ac16/casjobs.py#L296-L317
[ "def", "_options_dir", "(", "name", ")", ":", "_check_portname", "(", "name", ")", "_root", "=", "'/var/db/ports'", "# New path: /var/db/ports/category_portname", "new_dir", "=", "os", ".", "path", ".", "join", "(", "_root", ",", "name", ".", "replace", "(", "'/'", ",", "'_'", ")", ")", "# Old path: /var/db/ports/portname", "old_dir", "=", "os", ".", "path", ".", "join", "(", "_root", ",", "name", ".", "split", "(", "'/'", ")", "[", "-", "1", "]", ")", "if", "os", ".", "path", ".", "isdir", "(", "old_dir", ")", ":", "return", "old_dir", "return", "new_dir" ]
Drop a table from the MyDB context .
def drop_table ( self , table ) : job_id = self . submit ( "DROP TABLE %s" % table , context = "MYDB" ) status = self . monitor ( job_id ) if status [ 0 ] != 5 : raise Exception ( "Couldn't drop table %s" % table )
11,826
https://github.com/dfm/casjobs/blob/1cc3f5511cc254d776082909221787e3c037ac16/casjobs.py#L319-L331
[ "def", "write", "(", "self", ",", "value", ")", ":", "if", "not", "isinstance", "(", "value", ",", "bool", ")", ":", "raise", "TypeError", "(", "\"Invalid value type, should be bool.\"", ")", "# Write value", "try", ":", "if", "value", ":", "os", ".", "write", "(", "self", ".", "_fd", ",", "b\"1\\n\"", ")", "else", ":", "os", ".", "write", "(", "self", ".", "_fd", ",", "b\"0\\n\"", ")", "except", "OSError", "as", "e", ":", "raise", "GPIOError", "(", "e", ".", "errno", ",", "\"Writing GPIO: \"", "+", "e", ".", "strerror", ")", "# Rewind", "try", ":", "os", ".", "lseek", "(", "self", ".", "_fd", ",", "0", ",", "os", ".", "SEEK_SET", ")", "except", "OSError", "as", "e", ":", "raise", "GPIOError", "(", "e", ".", "errno", ",", "\"Rewinding GPIO: \"", "+", "e", ".", "strerror", ")" ]
Shorthand for counting the results of a specific query .
def count ( self , q ) : q = "SELECT COUNT(*) %s" % q return int ( self . quick ( q ) . split ( "\n" ) [ 1 ] )
11,827
https://github.com/dfm/casjobs/blob/1cc3f5511cc254d776082909221787e3c037ac16/casjobs.py#L333-L348
[ "def", "save", "(", "self", ",", "create_multiple_renditions", "=", "True", ",", "preserve_source_rendition", "=", "True", ",", "encode_to", "=", "enums", ".", "EncodeToEnum", ".", "FLV", ")", ":", "if", "is_ftp_connection", "(", "self", ".", "connection", ")", "and", "len", "(", "self", ".", "assets", ")", ">", "0", ":", "self", ".", "connection", ".", "post", "(", "xml", "=", "self", ".", "to_xml", "(", ")", ",", "assets", "=", "self", ".", "assets", ")", "elif", "not", "self", ".", "id", "and", "self", ".", "_filename", ":", "self", ".", "id", "=", "self", ".", "connection", ".", "post", "(", "'create_video'", ",", "self", ".", "_filename", ",", "create_multiple_renditions", "=", "create_multiple_renditions", ",", "preserve_source_rendition", "=", "preserve_source_rendition", ",", "encode_to", "=", "encode_to", ",", "video", "=", "self", ".", "_to_dict", "(", ")", ")", "elif", "not", "self", ".", "id", "and", "len", "(", "self", ".", "renditions", ")", ">", "0", ":", "self", ".", "id", "=", "self", ".", "connection", ".", "post", "(", "'create_video'", ",", "video", "=", "self", ".", "_to_dict", "(", ")", ")", "elif", "self", ".", "id", ":", "data", "=", "self", ".", "connection", ".", "post", "(", "'update_video'", ",", "video", "=", "self", ".", "_to_dict", "(", ")", ")", "if", "data", ":", "self", ".", "_load", "(", "data", ")" ]
Lists the tables in mydb .
def list_tables ( self ) : q = 'SELECT Distinct TABLE_NAME FROM information_schema.TABLES' res = self . quick ( q , context = 'MYDB' , task_name = 'listtables' , system = True ) # the first line is a header and the last is always empty # also, the table names have " as the first and last characters return [ l [ 1 : - 1 ] for l in res . split ( '\n' ) [ 1 : - 1 ] ]
11,828
https://github.com/dfm/casjobs/blob/1cc3f5511cc254d776082909221787e3c037ac16/casjobs.py#L350-L362
[ "def", "aggregate_registry_timers", "(", ")", ":", "import", "itertools", "timers", "=", "sorted", "(", "shared_registry", ".", "values", "(", ")", ",", "key", "=", "lambda", "t", ":", "t", ".", "desc", ")", "aggregate_timers", "=", "[", "]", "for", "k", ",", "g", "in", "itertools", ".", "groupby", "(", "timers", ",", "key", "=", "lambda", "t", ":", "t", ".", "desc", ")", ":", "group", "=", "list", "(", "g", ")", "num_calls", "=", "len", "(", "group", ")", "total_elapsed_ms", "=", "sum", "(", "t", ".", "elapsed_time_ms", "for", "t", "in", "group", ")", "first_start_time", "=", "min", "(", "t", ".", "start_time", "for", "t", "in", "group", ")", "# We'll use the first start time as a sort key.", "aggregate_timers", ".", "append", "(", "(", "first_start_time", ",", "(", "k", ",", "total_elapsed_ms", ",", "num_calls", ")", ")", ")", "aggregate_timers", ".", "sort", "(", ")", "return", "zip", "(", "*", "aggregate_timers", ")", "[", "1", "]" ]
Multiply the given number n by some configured multiplier and then add a configured offset .
def multiply_and_add ( n ) : multiplier , offset = di . resolver . unpack ( multiply_and_add ) return ( multiplier * n ) + offset
11,829
https://github.com/ncraike/fang/blob/2d9e1216c866e450059017f83ab775f7716eda7a/examples/multiple_dependencies.py#L13-L17
[ "def", "delete_session_entity_type", "(", "project_id", ",", "session_id", ",", "entity_type_display_name", ")", ":", "import", "dialogflow_v2", "as", "dialogflow", "session_entity_types_client", "=", "dialogflow", ".", "SessionEntityTypesClient", "(", ")", "session_entity_type_name", "=", "(", "session_entity_types_client", ".", "session_entity_type_path", "(", "project_id", ",", "session_id", ",", "entity_type_display_name", ")", ")", "session_entity_types_client", ".", "delete_session_entity_type", "(", "session_entity_type_name", ")" ]
Flush the buffer of the tail
def flush_buffer ( self ) : if len ( self . buffer ) > 0 : return_value = '' . join ( self . buffer ) self . buffer . clear ( ) self . send_message ( return_value ) self . last_flush_date = datetime . datetime . now ( )
11,830
https://github.com/mastro35/flows/blob/05e488385673a69597b5b39c7728795aa4d5eb18/flows/Actions/InputTailAction.py#L64-L70
[ "def", "get_community_names", "(", ")", ":", "ret", "=", "dict", "(", ")", "# Look in GPO settings first", "if", "__utils__", "[", "'reg.key_exists'", "]", "(", "_HKEY", ",", "_COMMUNITIES_GPO_KEY", ")", ":", "_LOG", ".", "debug", "(", "'Loading communities from Group Policy settings'", ")", "current_values", "=", "__utils__", "[", "'reg.list_values'", "]", "(", "_HKEY", ",", "_COMMUNITIES_GPO_KEY", ",", "include_default", "=", "False", ")", "# GPO settings are different in that they do not designate permissions", "# They are a numbered list of communities like so:", "#", "# {1: \"community 1\",", "# 2: \"community 2\"}", "#", "# Denote that it is being managed by Group Policy.", "#", "# community 1:", "# Managed by GPO", "# community 2:", "# Managed by GPO", "if", "isinstance", "(", "current_values", ",", "list", ")", ":", "for", "current_value", "in", "current_values", ":", "# Ignore error values", "if", "not", "isinstance", "(", "current_value", ",", "dict", ")", ":", "continue", "ret", "[", "current_value", "[", "'vdata'", "]", "]", "=", "'Managed by GPO'", "if", "not", "ret", ":", "_LOG", ".", "debug", "(", "'Loading communities from SNMP settings'", ")", "current_values", "=", "__utils__", "[", "'reg.list_values'", "]", "(", "_HKEY", ",", "_COMMUNITIES_KEY", ",", "include_default", "=", "False", ")", "# The communities are stored as the community name with a numeric", "# permission value. Like this (4 = Read Only):", "#", "# {\"community 1\": 4,", "# \"community 2\": 4}", "#", "# Convert the numeric value to the text equivalent, as present in the", "# Windows SNMP service GUI.", "#", "# community 1:", "# Read Only", "# community 2:", "# Read Only", "if", "isinstance", "(", "current_values", ",", "list", ")", ":", "for", "current_value", "in", "current_values", ":", "# Ignore error values", "if", "not", "isinstance", "(", "current_value", ",", "dict", ")", ":", "continue", "permissions", "=", "six", ".", "text_type", "(", ")", "for", "permission_name", "in", "_PERMISSION_TYPES", ":", "if", "current_value", "[", "'vdata'", "]", "==", "_PERMISSION_TYPES", "[", "permission_name", "]", ":", "permissions", "=", "permission_name", "break", "ret", "[", "current_value", "[", "'vname'", "]", "]", "=", "permissions", "if", "not", "ret", ":", "_LOG", ".", "debug", "(", "'Unable to find existing communities.'", ")", "return", "ret" ]
Conveniently set one or more fields at a time .
def set ( self , * args , * * kwargs ) : if args : for arg in args : if arg is not None : for name in self . __slots__ : self . _set ( name , getattr ( arg , name , UNSET ) ) for name in kwargs : self . _set ( name , kwargs . get ( name , UNSET ) )
11,831
https://github.com/zsimic/runez/blob/14363b719a1aae1528859a501a22d075ce0abfcc/src/runez/base.py#L105-L118
[ "def", "get_kmgraph_meta", "(", "mapper_summary", ")", ":", "d", "=", "mapper_summary", "[", "\"custom_meta\"", "]", "meta", "=", "(", "\"<b>N_cubes:</b> \"", "+", "str", "(", "d", "[", "\"n_cubes\"", "]", ")", "+", "\" <b>Perc_overlap:</b> \"", "+", "str", "(", "d", "[", "\"perc_overlap\"", "]", ")", ")", "meta", "+=", "(", "\"<br><b>Nodes:</b> \"", "+", "str", "(", "mapper_summary", "[", "\"n_nodes\"", "]", ")", "+", "\" <b>Edges:</b> \"", "+", "str", "(", "mapper_summary", "[", "\"n_edges\"", "]", ")", "+", "\" <b>Total samples:</b> \"", "+", "str", "(", "mapper_summary", "[", "\"n_total\"", "]", ")", "+", "\" <b>Unique_samples:</b> \"", "+", "str", "(", "mapper_summary", "[", "\"n_unique\"", "]", ")", ")", "return", "meta" ]
Enable contextual logging
def enable ( self ) : with self . _lock : if self . filter is None : self . filter = self . _filter_type ( self )
11,832
https://github.com/zsimic/runez/blob/14363b719a1aae1528859a501a22d075ce0abfcc/src/runez/base.py#L161-L165
[ "def", "main", "(", ")", ":", "fmt", "=", "'svg'", "title", "=", "\"\"", "if", "'-h'", "in", "sys", ".", "argv", ":", "print", "(", "main", ".", "__doc__", ")", "sys", ".", "exit", "(", ")", "if", "'-f'", "in", "sys", ".", "argv", ":", "ind", "=", "sys", ".", "argv", ".", "index", "(", "'-f'", ")", "file", "=", "sys", ".", "argv", "[", "ind", "+", "1", "]", "X", "=", "numpy", ".", "loadtxt", "(", "file", ")", "file", "=", "sys", ".", "argv", "[", "ind", "+", "2", "]", "X2", "=", "numpy", ".", "loadtxt", "(", "file", ")", "# else:", "# X=numpy.loadtxt(sys.stdin,dtype=numpy.float)", "else", ":", "print", "(", "'-f option required'", ")", "print", "(", "main", ".", "__doc__", ")", "sys", ".", "exit", "(", ")", "if", "'-fmt'", "in", "sys", ".", "argv", ":", "ind", "=", "sys", ".", "argv", ".", "index", "(", "'-fmt'", ")", "fmt", "=", "sys", ".", "argv", "[", "ind", "+", "1", "]", "if", "'-t'", "in", "sys", ".", "argv", ":", "ind", "=", "sys", ".", "argv", ".", "index", "(", "'-t'", ")", "title", "=", "sys", ".", "argv", "[", "ind", "+", "1", "]", "CDF", "=", "{", "'X'", ":", "1", "}", "pmagplotlib", ".", "plot_init", "(", "CDF", "[", "'X'", "]", ",", "5", ",", "5", ")", "pmagplotlib", ".", "plot_cdf", "(", "CDF", "[", "'X'", "]", ",", "X", ",", "''", ",", "'r'", ",", "''", ")", "pmagplotlib", ".", "plot_cdf", "(", "CDF", "[", "'X'", "]", ",", "X2", ",", "title", ",", "'b'", ",", "''", ")", "D", ",", "p", "=", "scipy", ".", "stats", ".", "ks_2samp", "(", "X", ",", "X2", ")", "if", "p", ">=", ".05", ":", "print", "(", "D", ",", "p", ",", "' not rejected at 95%'", ")", "else", ":", "print", "(", "D", ",", "p", ",", "' rejected at 95%'", ")", "pmagplotlib", ".", "draw_figs", "(", "CDF", ")", "ans", "=", "input", "(", "'S[a]ve plot, <Return> to quit '", ")", "if", "ans", "==", "'a'", ":", "files", "=", "{", "'X'", ":", "'CDF_.'", "+", "fmt", "}", "pmagplotlib", ".", "save_plots", "(", "CDF", ",", "files", ")" ]
Set current thread s logging context to specified values
def set_threadlocal ( self , * * values ) : with self . _lock : self . _ensure_threadlocal ( ) self . _tpayload . context = values
11,833
https://github.com/zsimic/runez/blob/14363b719a1aae1528859a501a22d075ce0abfcc/src/runez/base.py#L175-L179
[ "def", "is_ome", "(", "self", ")", ":", "if", "self", ".", "index", ">", "1", "or", "not", "self", ".", "description", ":", "return", "False", "d", "=", "self", ".", "description", "return", "d", "[", ":", "14", "]", "==", "'<?xml version='", "and", "d", "[", "-", "6", ":", "]", "==", "'</OME>'" ]
Add values to current thread s logging context
def add_threadlocal ( self , * * values ) : with self . _lock : self . _ensure_threadlocal ( ) self . _tpayload . context . update ( * * values )
11,834
https://github.com/zsimic/runez/blob/14363b719a1aae1528859a501a22d075ce0abfcc/src/runez/base.py#L181-L185
[ "def", "parse_torrent_properties", "(", "table_datas", ")", ":", "output", "=", "{", "'category'", ":", "table_datas", "[", "0", "]", ".", "text", ",", "'subcategory'", ":", "None", ",", "'quality'", ":", "None", ",", "'language'", ":", "None", "}", "for", "i", "in", "range", "(", "1", ",", "len", "(", "table_datas", ")", ")", ":", "td", "=", "table_datas", "[", "i", "]", "url", "=", "td", ".", "get", "(", "'href'", ")", "params", "=", "Parser", ".", "get_params", "(", "url", ")", "if", "Parser", ".", "is_subcategory", "(", "params", ")", "and", "not", "output", "[", "'subcategory'", "]", ":", "output", "[", "'subcategory'", "]", "=", "td", ".", "text", "elif", "Parser", ".", "is_quality", "(", "params", ")", "and", "not", "output", "[", "'quality'", "]", ":", "output", "[", "'quality'", "]", "=", "td", ".", "text", "elif", "Parser", ".", "is_language", "(", "params", ")", "and", "not", "output", "[", "'language'", "]", ":", "output", "[", "'language'", "]", "=", "td", ".", "text", "return", "output" ]
Add values to global logging context
def add_global ( self , * * values ) : with self . _lock : self . _ensure_global ( ) self . _gpayload . update ( * * values )
11,835
https://github.com/zsimic/runez/blob/14363b719a1aae1528859a501a22d075ce0abfcc/src/runez/base.py#L209-L213
[ "def", "calc_actualremoterelieve_v1", "(", "self", ")", ":", "con", "=", "self", ".", "parameters", ".", "control", ".", "fastaccess", "flu", "=", "self", ".", "sequences", ".", "fluxes", ".", "fastaccess", "d_smoothpar", "=", "con", ".", "remoterelievetolerance", "*", "flu", ".", "allowedremoterelieve", "flu", ".", "actualremoterelieve", "=", "smoothutils", ".", "smooth_min1", "(", "flu", ".", "possibleremoterelieve", ",", "flu", ".", "allowedremoterelieve", ",", "d_smoothpar", ")", "for", "dummy", "in", "range", "(", "5", ")", ":", "d_smoothpar", "/=", "5.", "flu", ".", "actualremoterelieve", "=", "smoothutils", ".", "smooth_max1", "(", "flu", ".", "actualremoterelieve", ",", "0.", ",", "d_smoothpar", ")", "d_smoothpar", "/=", "5.", "flu", ".", "actualremoterelieve", "=", "smoothutils", ".", "smooth_min1", "(", "flu", ".", "actualremoterelieve", ",", "flu", ".", "possibleremoterelieve", ",", "d_smoothpar", ")", "flu", ".", "actualremoterelieve", "=", "min", "(", "flu", ".", "actualremoterelieve", ",", "flu", ".", "possibleremoterelieve", ")", "flu", ".", "actualremoterelieve", "=", "min", "(", "flu", ".", "actualremoterelieve", ",", "flu", ".", "allowedremoterelieve", ")", "flu", ".", "actualremoterelieve", "=", "max", "(", "flu", ".", "actualremoterelieve", ",", "0.", ")" ]
Set visible = True to the terminal carbon atoms .
def display_terminal_carbon ( mol ) : for i , a in mol . atoms_iter ( ) : if mol . neighbor_count ( i ) == 1 : a . visible = True
11,836
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/draw/helper.py#L16-L21
[ "def", "_timestamp_regulator", "(", "self", ")", ":", "unified_timestamps", "=", "_PrettyDefaultDict", "(", "list", ")", "staged_files", "=", "self", ".", "_list_audio_files", "(", "sub_dir", "=", "\"staging\"", ")", "for", "timestamp_basename", "in", "self", ".", "__timestamps_unregulated", ":", "if", "len", "(", "self", ".", "__timestamps_unregulated", "[", "timestamp_basename", "]", ")", ">", "1", ":", "# File has been splitted", "timestamp_name", "=", "''", ".", "join", "(", "timestamp_basename", ".", "split", "(", "'.'", ")", "[", ":", "-", "1", "]", ")", "staged_splitted_files_of_timestamp", "=", "list", "(", "filter", "(", "lambda", "staged_file", ":", "(", "timestamp_name", "==", "staged_file", "[", ":", "-", "3", "]", "and", "all", "(", "[", "(", "x", "in", "set", "(", "map", "(", "str", ",", "range", "(", "10", ")", ")", ")", ")", "for", "x", "in", "staged_file", "[", "-", "3", ":", "]", "]", ")", ")", ",", "staged_files", ")", ")", "if", "len", "(", "staged_splitted_files_of_timestamp", ")", "==", "0", ":", "self", ".", "__errors", "[", "(", "time", "(", ")", ",", "timestamp_basename", ")", "]", "=", "{", "\"reason\"", ":", "\"Missing staged file\"", ",", "\"current_staged_files\"", ":", "staged_files", "}", "continue", "staged_splitted_files_of_timestamp", ".", "sort", "(", ")", "unified_timestamp", "=", "list", "(", ")", "for", "staging_digits", ",", "splitted_file", "in", "enumerate", "(", "self", ".", "__timestamps_unregulated", "[", "timestamp_basename", "]", ")", ":", "prev_splits_sec", "=", "0", "if", "int", "(", "staging_digits", ")", "!=", "0", ":", "prev_splits_sec", "=", "self", ".", "_get_audio_duration_seconds", "(", "\"{}/staging/{}{:03d}\"", ".", "format", "(", "self", ".", "src_dir", ",", "timestamp_name", ",", "staging_digits", "-", "1", ")", ")", "for", "word_block", "in", "splitted_file", ":", "unified_timestamp", ".", "append", "(", "_WordBlock", "(", "word", "=", "word_block", ".", "word", ",", "start", "=", "round", "(", "word_block", ".", "start", "+", "prev_splits_sec", ",", "2", ")", ",", "end", "=", "round", "(", "word_block", ".", "end", "+", "prev_splits_sec", ",", "2", ")", ")", ")", "unified_timestamps", "[", "str", "(", "timestamp_basename", ")", "]", "+=", "unified_timestamp", "else", ":", "unified_timestamps", "[", "timestamp_basename", "]", "+=", "self", ".", "__timestamps_unregulated", "[", "timestamp_basename", "]", "[", "0", "]", "self", ".", "__timestamps", ".", "update", "(", "unified_timestamps", ")", "self", ".", "__timestamps_unregulated", "=", "_PrettyDefaultDict", "(", "list", ")" ]
Show equalized double bond if it is connected to terminal atom .
def equalize_terminal_double_bond ( mol ) : for i , a in mol . atoms_iter ( ) : if mol . neighbor_count ( i ) == 1 : nb = list ( mol . neighbors ( i ) . values ( ) ) [ 0 ] if nb . order == 2 : nb . type = 2
11,837
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/draw/helper.py#L24-L31
[ "def", "table_to_gwf", "(", "table", ",", "filename", ",", "name", ",", "*", "*", "kwargs", ")", ":", "from", "LDAStools", ".", "frameCPP", "import", "(", "FrEvent", ",", "GPSTime", ")", "# create frame", "write_kw", "=", "{", "key", ":", "kwargs", ".", "pop", "(", "key", ")", "for", "key", "in", "(", "'compression'", ",", "'compression_level'", ")", "if", "key", "in", "kwargs", "}", "frame", "=", "io_gwf", ".", "create_frame", "(", "name", "=", "name", ",", "*", "*", "kwargs", ")", "# append row by row", "names", "=", "table", ".", "dtype", ".", "names", "for", "row", "in", "table", ":", "rowd", "=", "dict", "(", "(", "n", ",", "row", "[", "n", "]", ")", "for", "n", "in", "names", ")", "gps", "=", "LIGOTimeGPS", "(", "rowd", ".", "pop", "(", "'time'", ",", "0", ")", ")", "frame", ".", "AppendFrEvent", "(", "FrEvent", "(", "str", "(", "name", ")", ",", "str", "(", "rowd", ".", "pop", "(", "'comment'", ",", "''", ")", ")", ",", "str", "(", "rowd", ".", "pop", "(", "'inputs'", ",", "''", ")", ")", ",", "GPSTime", "(", "gps", ".", "gpsSeconds", ",", "gps", ".", "gpsNanoSeconds", ")", ",", "float", "(", "rowd", ".", "pop", "(", "'timeBefore'", ",", "0", ")", ")", ",", "float", "(", "rowd", ".", "pop", "(", "'timeAfter'", ",", "0", ")", ")", ",", "int", "(", "rowd", ".", "pop", "(", "'eventStatus'", ",", "0", ")", ")", ",", "float", "(", "rowd", ".", "pop", "(", "'amplitude'", ",", "0", ")", ")", ",", "float", "(", "rowd", ".", "pop", "(", "'probability'", ",", "-", "1", ")", ")", ",", "str", "(", "rowd", ".", "pop", "(", "'statistics'", ",", "''", ")", ")", ",", "list", "(", "rowd", ".", "items", "(", ")", ")", ",", "# remaining params as tuple", ")", ")", "# write frame to file", "io_gwf", ".", "write_frames", "(", "filename", ",", "[", "frame", "]", ",", "*", "*", "write_kw", ")" ]
Arrange stereo wedge direction from spine to terminal atom
def spine_to_terminal_wedge ( mol ) : for i , a in mol . atoms_iter ( ) : if mol . neighbor_count ( i ) == 1 : ni , nb = list ( mol . neighbors ( i ) . items ( ) ) [ 0 ] if nb . order == 1 and nb . type in ( 1 , 2 ) and ni > i != nb . is_lower_first : nb . is_lower_first = not nb . is_lower_first nb . type = { 1 : 2 , 2 : 1 } [ nb . type ]
11,838
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/draw/helper.py#L34-L43
[ "def", "load_data", "(", "self", ")", ":", "data", "=", "[", "]", "valid_dates", "=", "[", "]", "mrms_files", "=", "np", ".", "array", "(", "sorted", "(", "os", ".", "listdir", "(", "self", ".", "path", "+", "self", ".", "variable", "+", "\"/\"", ")", ")", ")", "mrms_file_dates", "=", "np", ".", "array", "(", "[", "m_file", ".", "split", "(", "\"_\"", ")", "[", "-", "2", "]", ".", "split", "(", "\"-\"", ")", "[", "0", "]", "for", "m_file", "in", "mrms_files", "]", ")", "old_mrms_file", "=", "None", "file_obj", "=", "None", "for", "t", "in", "range", "(", "self", ".", "all_dates", ".", "shape", "[", "0", "]", ")", ":", "file_index", "=", "np", ".", "where", "(", "mrms_file_dates", "==", "self", ".", "all_dates", "[", "t", "]", ".", "strftime", "(", "\"%Y%m%d\"", ")", ")", "[", "0", "]", "if", "len", "(", "file_index", ")", ">", "0", ":", "mrms_file", "=", "mrms_files", "[", "file_index", "]", "[", "0", "]", "if", "mrms_file", "is", "not", "None", ":", "if", "file_obj", "is", "not", "None", ":", "file_obj", ".", "close", "(", ")", "file_obj", "=", "Dataset", "(", "self", ".", "path", "+", "self", ".", "variable", "+", "\"/\"", "+", "mrms_file", ")", "#old_mrms_file = mrms_file", "if", "\"time\"", "in", "file_obj", ".", "variables", ".", "keys", "(", ")", ":", "time_var", "=", "\"time\"", "else", ":", "time_var", "=", "\"date\"", "file_valid_dates", "=", "pd", ".", "DatetimeIndex", "(", "num2date", "(", "file_obj", ".", "variables", "[", "time_var", "]", "[", ":", "]", ",", "file_obj", ".", "variables", "[", "time_var", "]", ".", "units", ")", ")", "else", ":", "file_valid_dates", "=", "pd", ".", "DatetimeIndex", "(", "[", "]", ")", "time_index", "=", "np", ".", "where", "(", "file_valid_dates", ".", "values", "==", "self", ".", "all_dates", ".", "values", "[", "t", "]", ")", "[", "0", "]", "if", "len", "(", "time_index", ")", ">", "0", ":", "data", ".", "append", "(", "file_obj", ".", "variables", "[", "self", ".", "variable", "]", "[", "time_index", "[", "0", "]", "]", ")", "valid_dates", ".", "append", "(", "self", ".", "all_dates", "[", "t", "]", ")", "if", "file_obj", "is", "not", "None", ":", "file_obj", ".", "close", "(", ")", "self", ".", "data", "=", "np", ".", "array", "(", "data", ")", "self", ".", "data", "[", "self", ".", "data", "<", "0", "]", "=", "0", "self", ".", "data", "[", "self", ".", "data", ">", "150", "]", "=", "150", "self", ".", "valid_dates", "=", "pd", ".", "DatetimeIndex", "(", "valid_dates", ")" ]
Set double bonds around the ring .
def format_ring_double_bond ( mol ) : mol . require ( "Topology" ) mol . require ( "ScaleAndCenter" ) for r in sorted ( mol . rings , key = len , reverse = True ) : vertices = [ mol . atom ( n ) . coords for n in r ] try : if geometry . is_clockwise ( vertices ) : cpath = iterator . consecutive ( itertools . cycle ( r ) , 2 ) else : cpath = iterator . consecutive ( itertools . cycle ( reversed ( r ) ) , 2 ) except ValueError : continue for _ in r : u , v = next ( cpath ) b = mol . bond ( u , v ) if b . order == 2 : b . type = int ( ( u > v ) == b . is_lower_first )
11,839
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/draw/helper.py#L46-L64
[ "def", "load", "(", "self", ",", "days", "=", "PRELOAD_DAYS", ",", "only_cameras", "=", "None", ",", "date_from", "=", "None", ",", "date_to", "=", "None", ",", "limit", "=", "None", ")", ":", "videos", "=", "[", "]", "url", "=", "LIBRARY_ENDPOINT", "if", "not", "(", "date_from", "and", "date_to", ")", ":", "now", "=", "datetime", ".", "today", "(", ")", "date_from", "=", "(", "now", "-", "timedelta", "(", "days", "=", "days", ")", ")", ".", "strftime", "(", "'%Y%m%d'", ")", "date_to", "=", "now", ".", "strftime", "(", "'%Y%m%d'", ")", "params", "=", "{", "'dateFrom'", ":", "date_from", ",", "'dateTo'", ":", "date_to", "}", "data", "=", "self", ".", "_session", ".", "query", "(", "url", ",", "method", "=", "'POST'", ",", "extra_params", "=", "params", ")", ".", "get", "(", "'data'", ")", "# get all cameras to append to create ArloVideo object", "all_cameras", "=", "self", ".", "_session", ".", "cameras", "for", "video", "in", "data", ":", "# pylint: disable=cell-var-from-loop", "srccam", "=", "list", "(", "filter", "(", "lambda", "cam", ":", "cam", ".", "device_id", "==", "video", ".", "get", "(", "'deviceId'", ")", ",", "all_cameras", ")", ")", "[", "0", "]", "# make sure only_cameras is a list", "if", "only_cameras", "and", "not", "isinstance", "(", "only_cameras", ",", "list", ")", ":", "only_cameras", "=", "[", "(", "only_cameras", ")", "]", "# filter by camera only", "if", "only_cameras", ":", "if", "list", "(", "filter", "(", "lambda", "cam", ":", "cam", ".", "device_id", "==", "srccam", ".", "device_id", ",", "list", "(", "only_cameras", ")", ")", ")", ":", "videos", ".", "append", "(", "ArloVideo", "(", "video", ",", "srccam", ",", "self", ".", "_session", ")", ")", "else", ":", "videos", ".", "append", "(", "ArloVideo", "(", "video", ",", "srccam", ",", "self", ".", "_session", ")", ")", "if", "limit", ":", "return", "videos", "[", ":", "limit", "]", "return", "videos" ]
Shortcut function to prepare molecule to draw . Overwrite this function for customized appearance . It is recommended to clone the molecule before draw because all the methods above are destructive .
def ready_to_draw ( mol ) : copied = molutil . clone ( mol ) # display_terminal_carbon(mol) equalize_terminal_double_bond ( copied ) # spine_to_terminal_wedge(copied) scale_and_center ( copied ) format_ring_double_bond ( copied ) return copied
11,840
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/draw/helper.py#L113-L125
[ "def", "RunValidationOutputToConsole", "(", "feed", ",", "options", ")", ":", "accumulator", "=", "CountingConsoleProblemAccumulator", "(", "options", ".", "error_types_ignore_list", ")", "problems", "=", "transitfeed", ".", "ProblemReporter", "(", "accumulator", ")", "_", ",", "exit_code", "=", "RunValidation", "(", "feed", ",", "options", ",", "problems", ")", "return", "exit_code" ]
Update dict from the attributes of a module class or other object .
def update_from_object ( self , obj , criterion = lambda key : key . isupper ( ) ) : log . debug ( 'Loading config from {0}' . format ( obj ) ) if isinstance ( obj , basestring ) : if '.' in obj : path , name = obj . rsplit ( '.' , 1 ) mod = __import__ ( path , globals ( ) , locals ( ) , [ name ] , 0 ) obj = getattr ( mod , name ) else : obj = __import__ ( obj , globals ( ) , locals ( ) , [ ] , 0 ) self . update ( ( key , getattr ( obj , key ) ) for key in filter ( criterion , dir ( obj ) ) )
11,841
https://github.com/adblair/configloader/blob/c56eb568a376243400bb72992ca927c35922c827/configloader/__init__.py#L46-L73
[ "def", "_process_pore_voxels", "(", "self", ")", ":", "num_Ps", "=", "self", ".", "num_pores", "(", ")", "pore_vox", "=", "sp", ".", "zeros", "(", "num_Ps", ",", "dtype", "=", "int", ")", "fiber_vox", "=", "sp", ".", "zeros", "(", "num_Ps", ",", "dtype", "=", "int", ")", "pore_space", "=", "self", ".", "_hull_image", ".", "copy", "(", ")", "fiber_space", "=", "self", ".", "_hull_image", ".", "copy", "(", ")", "pore_space", "[", "self", ".", "_fiber_image", "==", "0", "]", "=", "-", "1", "fiber_space", "[", "self", ".", "_fiber_image", "==", "1", "]", "=", "-", "1", "freq_pore_vox", "=", "itemfreq", "(", "pore_space", ")", "freq_pore_vox", "=", "freq_pore_vox", "[", "freq_pore_vox", "[", ":", ",", "0", "]", ">", "-", "1", "]", "freq_fiber_vox", "=", "itemfreq", "(", "fiber_space", ")", "freq_fiber_vox", "=", "freq_fiber_vox", "[", "freq_fiber_vox", "[", ":", ",", "0", "]", ">", "-", "1", "]", "pore_vox", "[", "freq_pore_vox", "[", ":", ",", "0", "]", "]", "=", "freq_pore_vox", "[", ":", ",", "1", "]", "fiber_vox", "[", "freq_fiber_vox", "[", ":", ",", "0", "]", "]", "=", "freq_fiber_vox", "[", ":", ",", "1", "]", "self", "[", "'pore.volume'", "]", "=", "pore_vox", "*", "self", ".", "network", ".", "resolution", "**", "3", "del", "pore_space", "del", "fiber_space" ]
Update dict from any environment variables that have a given prefix .
def update_from_env_namespace ( self , namespace ) : self . update ( ConfigLoader ( os . environ ) . namespace ( namespace ) )
11,842
https://github.com/adblair/configloader/blob/c56eb568a376243400bb72992ca927c35922c827/configloader/__init__.py#L119-L137
[ "def", "get_joint_sections", "(", "section", ",", "include_instructor_not_on_time_schedule", "=", "True", ")", ":", "joint_sections", "=", "[", "]", "for", "url", "in", "section", ".", "joint_section_urls", ":", "section", "=", "get_section_by_url", "(", "url", ",", "include_instructor_not_on_time_schedule", ")", "joint_sections", ".", "append", "(", "section", ")", "return", "joint_sections" ]
Update dict from several sources at once .
def update_from ( self , obj = None , yaml_env = None , yaml_file = None , json_env = None , json_file = None , env_namespace = None , ) : if obj : self . update_from_object ( obj ) if yaml_env : self . update_from_yaml_env ( yaml_env ) if yaml_file : self . update_from_yaml_file ( yaml_file ) if json_env : self . update_from_json_env ( json_env ) if json_file : self . update_from_json_file ( json_file ) if env_namespace : self . update_from_env_namespace ( env_namespace )
11,843
https://github.com/adblair/configloader/blob/c56eb568a376243400bb72992ca927c35922c827/configloader/__init__.py#L139-L179
[ "def", "multivariate_neg_logposterior", "(", "self", ",", "beta", ")", ":", "post", "=", "self", ".", "neg_loglik", "(", "beta", ")", "for", "k", "in", "range", "(", "0", ",", "self", ".", "z_no", ")", ":", "if", "self", ".", "latent_variables", ".", "z_list", "[", "k", "]", ".", "prior", ".", "covariance_prior", "is", "True", ":", "post", "+=", "-", "self", ".", "latent_variables", ".", "z_list", "[", "k", "]", ".", "prior", ".", "logpdf", "(", "self", ".", "custom_covariance", "(", "beta", ")", ")", "break", "else", ":", "post", "+=", "-", "self", ".", "latent_variables", ".", "z_list", "[", "k", "]", ".", "prior", ".", "logpdf", "(", "beta", "[", "k", "]", ")", "return", "post" ]
Return a copy with only the keys from a given namespace .
def namespace ( self , namespace , key_transform = lambda key : key ) : namespace = namespace . rstrip ( '_' ) + '_' return ConfigLoader ( ( key_transform ( key [ len ( namespace ) : ] ) , value ) for key , value in self . items ( ) if key [ : len ( namespace ) ] == namespace )
11,844
https://github.com/adblair/configloader/blob/c56eb568a376243400bb72992ca927c35922c827/configloader/__init__.py#L181-L208
[ "def", "find_best_frametype", "(", "channel", ",", "start", ",", "end", ",", "frametype_match", "=", "None", ",", "allow_tape", "=", "True", ",", "connection", "=", "None", ",", "host", "=", "None", ",", "port", "=", "None", ")", ":", "try", ":", "return", "find_frametype", "(", "channel", ",", "gpstime", "=", "(", "start", ",", "end", ")", ",", "frametype_match", "=", "frametype_match", ",", "allow_tape", "=", "allow_tape", ",", "on_gaps", "=", "'error'", ",", "connection", "=", "connection", ",", "host", "=", "host", ",", "port", "=", "port", ")", "except", "RuntimeError", ":", "# gaps (or something else went wrong)", "ftout", "=", "find_frametype", "(", "channel", ",", "gpstime", "=", "(", "start", ",", "end", ")", ",", "frametype_match", "=", "frametype_match", ",", "return_all", "=", "True", ",", "allow_tape", "=", "allow_tape", ",", "on_gaps", "=", "'ignore'", ",", "connection", "=", "connection", ",", "host", "=", "host", ",", "port", "=", "port", ")", "try", ":", "if", "isinstance", "(", "ftout", ",", "dict", ")", ":", "return", "{", "key", ":", "ftout", "[", "key", "]", "[", "0", "]", "for", "key", "in", "ftout", "}", "return", "ftout", "[", "0", "]", "except", "IndexError", ":", "raise", "ValueError", "(", "\"Cannot find any valid frametypes for channel(s)\"", ")" ]
Return a copy with only the keys from a given namespace lower - cased .
def namespace_lower ( self , namespace ) : return self . namespace ( namespace , key_transform = lambda key : key . lower ( ) )
11,845
https://github.com/adblair/configloader/blob/c56eb568a376243400bb72992ca927c35922c827/configloader/__init__.py#L210-L236
[ "def", "remove_pickle_problems", "(", "obj", ")", ":", "if", "hasattr", "(", "obj", ",", "\"doc_loader\"", ")", ":", "obj", ".", "doc_loader", "=", "None", "if", "hasattr", "(", "obj", ",", "\"embedded_tool\"", ")", ":", "obj", ".", "embedded_tool", "=", "remove_pickle_problems", "(", "obj", ".", "embedded_tool", ")", "if", "hasattr", "(", "obj", ",", "\"steps\"", ")", ":", "obj", ".", "steps", "=", "[", "remove_pickle_problems", "(", "s", ")", "for", "s", "in", "obj", ".", "steps", "]", "return", "obj" ]
Render a diagram of the ETL pipeline
def render_diagram ( root_task , out_base , max_param_len = 20 , horizontal = False , colored = False ) : import re import codecs import subprocess from ozelot import config from ozelot . etl . tasks import get_task_name , get_task_param_string # the graph - lines in dot file lines = [ u"digraph G {" ] if horizontal : lines . append ( u"rankdir=LR;" ) # helper function: make unique task id from task name and parameters: # task name + parameter string, with spaces replaced with _ and all non-alphanumerical characters stripped def get_id ( task ) : s = get_task_name ( task ) + "_" + get_task_param_string ( task ) return re . sub ( r'\W+' , '' , re . sub ( ' ' , '_' , s ) ) # node names of tasks that have already been added to the graph existing_nodes = set ( ) # edge sets (tuples of two node names) that have already been added existing_edges = set ( ) # recursion function for generating the pipeline graph def _build ( task , parent_id = None ) : tid = get_id ( task ) # add node if it's not already there if tid not in existing_nodes : # build task label: task name plus dictionary of parameters as table params = task . to_str_params ( ) param_list = "" for k , v in params . items ( ) : # truncate param value if necessary, and add "..." if len ( v ) > max_param_len : v = v [ : max_param_len ] + "..." param_list += "<TR><TD ALIGN=\"LEFT\">" "<FONT POINT-SIZE=\"10\">{:s}</FONT>" "</TD><TD ALIGN=\"LEFT\">" "<FONT POINT-SIZE=\"10\">{:s}</FONT>" "</TD></TR>" . format ( k , v ) label = "<TABLE BORDER=\"0\" CELLSPACING=\"1\" CELLPADDING=\"1\">" "<TR><TD COLSPAN=\"2\" ALIGN=\"CENTER\">" "<FONT POINT-SIZE=\"12\">{:s}</FONT>" "</TD></TR>" "" . format ( get_task_name ( task ) ) + param_list + "</TABLE>" style = getattr ( task , 'diagram_style' , [ ] ) if colored : color = ', color="{:s}"' . format ( "green" if task . complete ( ) else "red" ) else : color = '' # add a node for the task lines . append ( u"{name:s} [label=< {label:s} >, shape=\"rect\" {color:s}, style=\"{style:s}\"];\n" u"" . format ( name = tid , label = label , color = color , style = ',' . join ( style ) ) ) existing_nodes . add ( tid ) # recurse over requirements for req in task . requires ( ) : _build ( req , parent_id = tid ) # add edge from current node to (upstream) parent, if it doesn't already exist if parent_id is not None and ( tid , parent_id ) not in existing_edges : lines . append ( u"{source:s} -> {target:s};\n" . format ( source = tid , target = parent_id ) ) # generate pipeline graph _build ( root_task ) # close the graph definition lines . append ( u"}" ) # write description in DOT format with codecs . open ( out_base + '.dot' , 'w' , encoding = 'utf-8' ) as f : f . write ( u"\n" . join ( lines ) ) # check existence of DOT_EXECUTABLE variable and file if not hasattr ( config , 'DOT_EXECUTABLE' ) : raise RuntimeError ( "Please configure the 'DOT_EXECUTABLE' variable in your 'project_config.py'" ) if not os . path . exists ( config . DOT_EXECUTABLE ) : raise IOError ( "Could not find file pointed to by 'DOT_EXECUTABLE': " + str ( config . DOT_EXECUTABLE ) ) # render to image using DOT # noinspection PyUnresolvedReferences subprocess . check_call ( [ config . DOT_EXECUTABLE , '-T' , 'png' , '-o' , out_base + '.png' , out_base + '.dot' ] )
11,846
https://github.com/ehansis/ozelot/blob/948675e02eb6fca940450f5cb814f53e97159e5b/ozelot/etl/util.py#L12-L127
[ "def", "_check_rest_version", "(", "self", ",", "version", ")", ":", "version", "=", "str", "(", "version", ")", "if", "version", "not", "in", "self", ".", "supported_rest_versions", ":", "msg", "=", "\"Library is incompatible with REST API version {0}\"", "raise", "ValueError", "(", "msg", ".", "format", "(", "version", ")", ")", "array_rest_versions", "=", "self", ".", "_list_available_rest_versions", "(", ")", "if", "version", "not", "in", "array_rest_versions", ":", "msg", "=", "\"Array is incompatible with REST API version {0}\"", "raise", "ValueError", "(", "msg", ".", "format", "(", "version", ")", ")", "return", "LooseVersion", "(", "version", ")" ]
Normalize a string
def sanitize ( s , normalize_whitespace = True , normalize_unicode = True , form = 'NFKC' , enforce_encoding = True , encoding = 'utf-8' ) : if enforce_encoding : s = s . encode ( encoding , errors = 'ignore' ) . decode ( encoding , errors = 'ignore' ) if normalize_unicode : s = unicodedata . normalize ( form , s ) if normalize_whitespace : s = re . sub ( r'\s+' , ' ' , s ) . strip ( ) return s
11,847
https://github.com/ehansis/ozelot/blob/948675e02eb6fca940450f5cb814f53e97159e5b/ozelot/etl/util.py#L130-L161
[ "def", "namer", "(", "cls", ",", "imageUrl", ",", "pageUrl", ")", ":", "start", "=", "''", "tsmatch", "=", "compile", "(", "r'/(\\d+)-'", ")", ".", "search", "(", "imageUrl", ")", "if", "tsmatch", ":", "start", "=", "datetime", ".", "utcfromtimestamp", "(", "int", "(", "tsmatch", ".", "group", "(", "1", ")", ")", ")", ".", "strftime", "(", "\"%Y-%m-%d\"", ")", "else", ":", "# There were only chapter 1, page 4 and 5 not matching when writing", "# this...", "start", "=", "'2015-04-11x'", "return", "start", "+", "\"-\"", "+", "pageUrl", ".", "rsplit", "(", "'/'", ",", "1", ")", "[", "-", "1", "]" ]
This is a shortcut for getting the sns_token as a post data of request body .
def get_ticket_for_sns_token ( self ) : self . logger . info ( "%s\t%s" % ( self . request_method , self . request_url ) ) return { "openid" : self . get_openid ( ) , "persistent_code" : self . get_persistent_code ( ) , }
11,848
https://github.com/gmdzy2010/dingtalk_sdk_gmdzy2010/blob/b06cb1f78f89be9554dcb6101af8bc72718a9ecd/dingtalk_sdk_gmdzy2010/authority_request.py#L86-L93
[ "def", "exclude_types", "(", "self", ",", "*", "objs", ")", ":", "for", "o", "in", "objs", ":", "for", "t", "in", "_keytuple", "(", "o", ")", ":", "if", "t", "and", "t", "not", "in", "self", ".", "_excl_d", ":", "self", ".", "_excl_d", "[", "t", "]", "=", "0" ]
Drop all tables for all models then re - create them
def reinitialize ( ) : from ozelot import client # import all additional models needed in this project # noinspection PyUnresolvedReferences from ozelot . orm . target import ORMTargetMarker client = client . get_client ( ) base . Base . drop_all ( client ) base . Base . create_all ( client )
11,849
https://github.com/ehansis/ozelot/blob/948675e02eb6fca940450f5cb814f53e97159e5b/examples/superheroes/superheroes/models.py#L130-L141
[ "def", "get_community_names", "(", ")", ":", "ret", "=", "dict", "(", ")", "# Look in GPO settings first", "if", "__utils__", "[", "'reg.key_exists'", "]", "(", "_HKEY", ",", "_COMMUNITIES_GPO_KEY", ")", ":", "_LOG", ".", "debug", "(", "'Loading communities from Group Policy settings'", ")", "current_values", "=", "__utils__", "[", "'reg.list_values'", "]", "(", "_HKEY", ",", "_COMMUNITIES_GPO_KEY", ",", "include_default", "=", "False", ")", "# GPO settings are different in that they do not designate permissions", "# They are a numbered list of communities like so:", "#", "# {1: \"community 1\",", "# 2: \"community 2\"}", "#", "# Denote that it is being managed by Group Policy.", "#", "# community 1:", "# Managed by GPO", "# community 2:", "# Managed by GPO", "if", "isinstance", "(", "current_values", ",", "list", ")", ":", "for", "current_value", "in", "current_values", ":", "# Ignore error values", "if", "not", "isinstance", "(", "current_value", ",", "dict", ")", ":", "continue", "ret", "[", "current_value", "[", "'vdata'", "]", "]", "=", "'Managed by GPO'", "if", "not", "ret", ":", "_LOG", ".", "debug", "(", "'Loading communities from SNMP settings'", ")", "current_values", "=", "__utils__", "[", "'reg.list_values'", "]", "(", "_HKEY", ",", "_COMMUNITIES_KEY", ",", "include_default", "=", "False", ")", "# The communities are stored as the community name with a numeric", "# permission value. Like this (4 = Read Only):", "#", "# {\"community 1\": 4,", "# \"community 2\": 4}", "#", "# Convert the numeric value to the text equivalent, as present in the", "# Windows SNMP service GUI.", "#", "# community 1:", "# Read Only", "# community 2:", "# Read Only", "if", "isinstance", "(", "current_values", ",", "list", ")", ":", "for", "current_value", "in", "current_values", ":", "# Ignore error values", "if", "not", "isinstance", "(", "current_value", ",", "dict", ")", ":", "continue", "permissions", "=", "six", ".", "text_type", "(", ")", "for", "permission_name", "in", "_PERMISSION_TYPES", ":", "if", "current_value", "[", "'vdata'", "]", "==", "_PERMISSION_TYPES", "[", "permission_name", "]", ":", "permissions", "=", "permission_name", "break", "ret", "[", "current_value", "[", "'vname'", "]", "]", "=", "permissions", "if", "not", "ret", ":", "_LOG", ".", "debug", "(", "'Unable to find existing communities.'", ")", "return", "ret" ]
This unwraps a decorated func returning the inner wrapped func .
def _unwrap_func ( cls , decorated_func ) : if click is not None : # Workaround for click.command() decorator not setting # __wrapped__ if isinstance ( decorated_func , click . Command ) : return cls . _unwrap_func ( decorated_func . callback ) if hasattr ( decorated_func , '__wrapped__' ) : # Recursion: unwrap more if needed return cls . _unwrap_func ( decorated_func . __wrapped__ ) else : # decorated_func isn't actually decorated, no more # unwrapping to do return decorated_func
11,850
https://github.com/ncraike/fang/blob/2d9e1216c866e450059017f83ab775f7716eda7a/fang/dependency_register.py#L21-L39
[ "def", "volumes_delete", "(", "storage_pool", ",", "logger", ")", ":", "try", ":", "for", "vol_name", "in", "storage_pool", ".", "listVolumes", "(", ")", ":", "try", ":", "vol", "=", "storage_pool", ".", "storageVolLookupByName", "(", "vol_name", ")", "vol", ".", "delete", "(", "0", ")", "except", "libvirt", ".", "libvirtError", ":", "logger", ".", "exception", "(", "\"Unable to delete storage volume %s.\"", ",", "vol_name", ")", "except", "libvirt", ".", "libvirtError", ":", "logger", ".", "exception", "(", "\"Unable to delete storage volumes.\"", ")" ]
Register a mapping of the dependent to resource name .
def _register_dependent ( self , dependent , resource_name ) : if dependent not in self . dependents : self . dependents [ dependent ] = [ ] self . dependents [ dependent ] . insert ( 0 , resource_name )
11,851
https://github.com/ncraike/fang/blob/2d9e1216c866e450059017f83ab775f7716eda7a/fang/dependency_register.py#L50-L59
[ "def", "communityvisibilitystate", "(", "self", ")", ":", "if", "self", ".", "_communityvisibilitystate", "==", "None", ":", "return", "None", "elif", "self", ".", "_communityvisibilitystate", "in", "self", ".", "VisibilityState", ":", "return", "self", ".", "VisibilityState", "[", "self", ".", "_communityvisibilitystate", "]", "else", ":", "#Invalid State", "return", "None" ]
Register the given dependent as depending on the resource named by resource_name .
def register ( self , resource_name , dependent = None ) : if dependent is None : # Give a partial usable as a decorator return partial ( self . register , resource_name ) dependent = self . _unwrap_dependent ( dependent ) self . _register_dependent ( dependent , resource_name ) self . _register_resource_dependency ( resource_name , dependent ) # Return dependent to ease use as decorator return dependent
11,852
https://github.com/ncraike/fang/blob/2d9e1216c866e450059017f83ab775f7716eda7a/fang/dependency_register.py#L66-L80
[ "def", "_create_auth", "(", "team", ",", "timeout", "=", "None", ")", ":", "url", "=", "get_registry_url", "(", "team", ")", "contents", "=", "_load_auth", "(", ")", "auth", "=", "contents", ".", "get", "(", "url", ")", "if", "auth", "is", "not", "None", ":", "# If the access token expires within a minute, update it.", "if", "auth", "[", "'expires_at'", "]", "<", "time", ".", "time", "(", ")", "+", "60", ":", "try", ":", "auth", "=", "_update_auth", "(", "team", ",", "auth", "[", "'refresh_token'", "]", ",", "timeout", ")", "except", "CommandException", "as", "ex", ":", "raise", "CommandException", "(", "\"Failed to update the access token (%s). Run `quilt login%s` again.\"", "%", "(", "ex", ",", "' '", "+", "team", "if", "team", "else", "''", ")", ")", "contents", "[", "url", "]", "=", "auth", "_save_auth", "(", "contents", ")", "return", "auth" ]
Runs OCSP verification and returns error code - 0 means success
def verify_ocsp ( cls , certificate , issuer ) : return OCSPVerifier ( certificate , issuer , cls . get_ocsp_url ( ) , cls . get_ocsp_responder_certificate_path ( ) ) . verify ( )
11,853
https://github.com/thorgate/django-esteid/blob/407ae513e357fedea0e3e42198df8eb9d9ff0646/esteid/middleware.py#L144-L150
[ "def", "set_bounds", "(", "self", ",", "new_bounds", ")", ":", "for", "row", ",", "key", "in", "enumerate", "(", "self", ".", "keys", ")", ":", "if", "key", "in", "new_bounds", ":", "self", ".", "_bounds", "[", "row", "]", "=", "new_bounds", "[", "key", "]" ]
Create a requests session that handles errors by retrying .
def requests_retry_session ( retries = 3 , backoff_factor = 0.3 , status_forcelist = ( 500 , 502 , 504 ) , session = None ) : session = session or requests . Session ( ) retry = Retry ( total = retries , read = retries , connect = retries , backoff_factor = backoff_factor , status_forcelist = status_forcelist , ) adapter = HTTPAdapter ( max_retries = retry ) session . mount ( 'http://' , adapter ) session . mount ( 'https://' , adapter ) return session
11,854
https://github.com/lsst-sqre/documenteer/blob/75f02901a80042b28d074df1cc1dca32eb8e38c8/documenteer/requestsutils.py#L11-L52
[ "def", "set_current", "(", "self", ",", "channel", ",", "value", ",", "unit", "=", "'A'", ")", ":", "dac_offset", "=", "self", ".", "_ch_cal", "[", "channel", "]", "[", "'DAC'", "]", "[", "'offset'", "]", "dac_gain", "=", "self", ".", "_ch_cal", "[", "channel", "]", "[", "'DAC'", "]", "[", "'gain'", "]", "if", "unit", "==", "'raw'", ":", "value", "=", "value", "elif", "unit", "==", "'A'", ":", "value", "=", "int", "(", "(", "-", "value", "*", "1000000", "-", "dac_offset", ")", "/", "dac_gain", ")", "# fix sign of output", "elif", "unit", "==", "'mA'", ":", "value", "=", "int", "(", "(", "-", "value", "*", "1000", "-", "dac_offset", ")", "/", "dac_gain", ")", "# fix sign of output", "elif", "unit", "==", "'uA'", ":", "value", "=", "int", "(", "(", "-", "value", "-", "dac_offset", ")", "/", "dac_gain", ")", "# fix sign of output", "else", ":", "raise", "TypeError", "(", "\"Invalid unit type.\"", ")", "self", ".", "_set_dac_value", "(", "channel", "=", "channel", ",", "value", "=", "value", ")" ]
Builds a dict of Sphinx configuration variables given a central configuration for LSST Design Documents and a metadata YAML file .
def configure_technote ( meta_stream ) : _metadata = yaml . load ( meta_stream ) confs = _build_confs ( _metadata ) return confs
11,855
https://github.com/lsst-sqre/documenteer/blob/75f02901a80042b28d074df1cc1dca32eb8e38c8/documenteer/sphinxconfig/technoteconf.py#L17-L67
[ "def", "shutdown", "(", "self", ",", "wait", "=", "True", ")", ":", "if", "self", ".", "__running", ":", "# Add a Non-entry for every worker thread we have.", "for", "thread", "in", "self", ".", "__threads", ":", "assert", "thread", ".", "isAlive", "(", ")", "self", ".", "__queue", ".", "append", "(", "None", ")", "self", ".", "__running", "=", "False", "if", "wait", ":", "self", ".", "__queue", ".", "wait", "(", ")", "for", "thread", "in", "self", ".", "__threads", ":", "thread", ".", "join", "(", ")" ]
Get ocsp responder certificate path
def ocsp_responder_certificate_path ( ) : certificate_path = getattr ( settings , 'ESTEID_OCSP_RESPONDER_CERTIFICATE_PATH' , 'TEST_of_SK_OCSP_RESPONDER_2011.pem' ) if certificate_path in [ 'TEST_of_SK_OCSP_RESPONDER_2011.pem' , 'sk-ocsp-responder-certificates.pem' ] : return os . path . join ( os . path . dirname ( __file__ ) , 'certs' , certificate_path ) return certificate_path
11,856
https://github.com/thorgate/django-esteid/blob/407ae513e357fedea0e3e42198df8eb9d9ff0646/esteid/config.py#L40-L55
[ "def", "_subtractSky", "(", "image", ",", "skyValue", ",", "memmap", "=", "False", ")", ":", "try", ":", "np", ".", "subtract", "(", "image", ".", "data", ",", "skyValue", ",", "image", ".", "data", ")", "except", "IOError", ":", "print", "(", "\"Unable to perform sky subtraction on data array\"", ")", "raise", "IOError" ]
Return a new Message instance . The arguments are passed to the marrow . mailer . Message constructor .
def new ( self , * * kwargs ) : app = self . app or current_app mailer = app . extensions [ 'marrowmailer' ] msg = mailer . new ( * * kwargs ) msg . __class__ = Message return msg
11,857
https://github.com/miguelgrinberg/Flask-MarrowMailer/blob/daf1ac0745fb31db2f43f4f7dc24c6f50ae96764/flask_marrowmailer.py#L62-L69
[ "def", "get_collision_state", "(", "self", ",", "collision_name", ")", ":", "return", "self", ".", "call_remote_api", "(", "'simxReadCollision'", ",", "self", ".", "get_collision_handle", "(", "collision_name", ")", ",", "streaming", "=", "True", ")" ]
Send the message . If message is an iterable then send all the messages .
def send ( self , msg ) : app = self . app or current_app mailer = app . extensions [ 'marrowmailer' ] mailer . start ( ) if not hasattr ( msg , '__iter__' ) : result = mailer . send ( msg ) else : result = map ( lambda message : mailer . send ( message ) , msg ) mailer . stop ( ) return result
11,858
https://github.com/miguelgrinberg/Flask-MarrowMailer/blob/daf1ac0745fb31db2f43f4f7dc24c6f50ae96764/flask_marrowmailer.py#L71-L82
[ "def", "generate_citation_counter", "(", "self", ")", ":", "cite_counter", "=", "dict", "(", ")", "filename", "=", "'%s.aux'", "%", "self", ".", "project_name", "with", "open", "(", "filename", ")", "as", "fobj", ":", "main_aux", "=", "fobj", ".", "read", "(", ")", "cite_counter", "[", "filename", "]", "=", "_count_citations", "(", "filename", ")", "for", "match", "in", "re", ".", "finditer", "(", "r'\\\\@input\\{(.*.aux)\\}'", ",", "main_aux", ")", ":", "filename", "=", "match", ".", "groups", "(", ")", "[", "0", "]", "try", ":", "counter", "=", "_count_citations", "(", "filename", ")", "except", "IOError", ":", "pass", "else", ":", "cite_counter", "[", "filename", "]", "=", "counter", "return", "cite_counter" ]
Returns the results of wdiff in a HTML compatible format .
def wdiff ( settings , wrap_with_html = False , fold_breaks = False , hard_breaks = False ) : diff = generate_wdiff ( settings . org_file , settings . new_file , fold_breaks ) if wrap_with_html : return wrap_content ( diff , settings , hard_breaks ) else : return diff
11,859
https://github.com/brutus/wdiffhtml/blob/e97b524a7945f7a626e33ec141343120c524d9fa/wdiffhtml/__init__.py#L62-L83
[ "def", "delete_persistent_data", "(", "role", ",", "zk_node", ")", ":", "if", "role", ":", "destroy_volumes", "(", "role", ")", "unreserve_resources", "(", "role", ")", "if", "zk_node", ":", "delete_zk_node", "(", "zk_node", ")" ]
Load settings from config file and return them as a dict . If the config file is not found or if it is invalid create and use a default config file .
def _load_config ( config_file ) : logger . debug ( 'Config file: {}' . format ( config_file ) ) parser = configparser . ConfigParser ( ) try : with config_file . open ( 'r' ) as f : parser . read_file ( f ) except FileNotFoundError as e : logger . warning ( 'Config file not found' ) parser = _use_default ( config_file ) except configparser . ParsingError as e : logger . warning ( 'Error in config file: {}' . format ( e ) ) parser = _use_default ( config_file ) finally : try : config = _load_options ( parser ) except ( configparser . NoOptionError ) : parser = _use_default ( config_file ) config = _load_options ( parser ) logger . debug ( 'Config loaded: {}' . format ( config_file ) ) return config
11,860
https://github.com/mesbahamin/chronophore/blob/ee140c61b4dfada966f078de8304bac737cec6f7/chronophore/config.py#L13-L44
[ "def", "incrementSub", "(", "self", ",", "amount", "=", "1", ")", ":", "self", ".", "_subProgressBar", ".", "setValue", "(", "self", ".", "subValue", "(", ")", "+", "amount", ")", "QApplication", ".", "instance", "(", ")", ".", "processEvents", "(", ")" ]
Load config options from parser and return them as a dict .
def _load_options ( parser ) : config = dict ( MESSAGE_DURATION = parser . getint ( 'gui' , 'message_duration' ) , GUI_WELCOME_LABLE = parser . get ( 'gui' , 'gui_welcome_label' ) , FULL_USER_NAMES = parser . getboolean ( 'gui' , 'full_user_names' ) , LARGE_FONT_SIZE = parser . getint ( 'gui' , 'large_font_size' ) , MEDIUM_FONT_SIZE = parser . getint ( 'gui' , 'medium_font_size' ) , SMALL_FONT_SIZE = parser . getint ( 'gui' , 'small_font_size' ) , TINY_FONT_SIZE = parser . getint ( 'gui' , 'tiny_font_size' ) , MAX_INPUT_LENGTH = parser . getint ( 'gui' , 'max_input_length' ) , ) return config
11,861
https://github.com/mesbahamin/chronophore/blob/ee140c61b4dfada966f078de8304bac737cec6f7/chronophore/config.py#L47-L63
[ "def", "get_free_project_name", "(", "self", ",", "base_name", ")", ":", "names", "=", "[", "p", ".", "name", "for", "p", "in", "self", ".", "_projects", ".", "values", "(", ")", "]", "if", "base_name", "not", "in", "names", ":", "return", "base_name", "i", "=", "1", "projects_path", "=", "self", ".", "projects_directory", "(", ")", "while", "True", ":", "new_name", "=", "\"{}-{}\"", ".", "format", "(", "base_name", ",", "i", ")", "if", "new_name", "not", "in", "names", "and", "not", "os", ".", "path", ".", "exists", "(", "os", ".", "path", ".", "join", "(", "projects_path", ",", "new_name", ")", ")", ":", "break", "i", "+=", "1", "if", "i", ">", "1000000", ":", "raise", "aiohttp", ".", "web", ".", "HTTPConflict", "(", "text", "=", "\"A project name could not be allocated (node limit reached?)\"", ")", "return", "new_name" ]
Write default values to a config file . If another config file already exists back it up before replacing it with the new file .
def _use_default ( config_file ) : default_config = OrderedDict ( ( ( 'gui' , OrderedDict ( ( ( 'message_duration' , 5 ) , ( 'gui_welcome_label' , 'Welcome to the STEM Learning Center!' ) , ( 'full_user_names' , True ) , ( 'large_font_size' , 30 ) , ( 'medium_font_size' , 18 ) , ( 'small_font_size' , 15 ) , ( 'tiny_font_size' , 10 ) , ( 'max_input_length' , 9 ) , ) ) , ) , ) ) parser = configparser . ConfigParser ( ) parser . read_dict ( default_config ) if config_file . exists ( ) : backup = config_file . with_suffix ( '.bak' ) os . rename ( str ( config_file ) , str ( backup ) ) logger . info ( '{} moved to {}.' . format ( config_file , backup ) ) with config_file . open ( 'w' ) as f : parser . write ( f ) logger . info ( 'Default config file created.' ) return parser
11,862
https://github.com/mesbahamin/chronophore/blob/ee140c61b4dfada966f078de8304bac737cec6f7/chronophore/config.py#L66-L104
[ "async", "def", "on_raw_422", "(", "self", ",", "message", ")", ":", "await", "self", ".", "_registration_completed", "(", "message", ")", "self", ".", "motd", "=", "None", "await", "self", ".", "on_connect", "(", ")" ]
Set an atom . Existing atom will be overwritten .
def add_atom ( self , key , atom ) : self . graph . add_node ( key , atom = atom )
11,863
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/model/graphmol.py#L79-L81
[ "def", "project_masks_on_boxes", "(", "segmentation_masks", ",", "proposals", ",", "discretization_size", ")", ":", "masks", "=", "[", "]", "M", "=", "discretization_size", "device", "=", "proposals", ".", "bbox", ".", "device", "proposals", "=", "proposals", ".", "convert", "(", "\"xyxy\"", ")", "assert", "segmentation_masks", ".", "size", "==", "proposals", ".", "size", ",", "\"{}, {}\"", ".", "format", "(", "segmentation_masks", ",", "proposals", ")", "# TODO put the proposals on the CPU, as the representation for the", "# masks is not efficient GPU-wise (possibly several small tensors for", "# representing a single instance mask)", "proposals", "=", "proposals", ".", "bbox", ".", "to", "(", "torch", ".", "device", "(", "\"cpu\"", ")", ")", "for", "segmentation_mask", ",", "proposal", "in", "zip", "(", "segmentation_masks", ",", "proposals", ")", ":", "# crop the masks, resize them to the desired resolution and", "# then convert them to the tensor representation,", "# instead of the list representation that was used", "cropped_mask", "=", "segmentation_mask", ".", "crop", "(", "proposal", ")", "scaled_mask", "=", "cropped_mask", ".", "resize", "(", "(", "M", ",", "M", ")", ")", "mask", "=", "scaled_mask", ".", "convert", "(", "mode", "=", "\"mask\"", ")", "masks", ".", "append", "(", "mask", ")", "if", "len", "(", "masks", ")", "==", "0", ":", "return", "torch", ".", "empty", "(", "0", ",", "dtype", "=", "torch", ".", "float32", ",", "device", "=", "device", ")", "return", "torch", ".", "stack", "(", "masks", ",", "dim", "=", "0", ")", ".", "to", "(", "device", ",", "dtype", "=", "torch", ".", "float32", ")" ]
Iterate over atoms .
def atoms_iter ( self ) : for n , atom in self . graph . nodes . data ( "atom" ) : yield n , atom
11,864
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/model/graphmol.py#L87-L90
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Set a bond . Existing bond will be overwritten .
def add_bond ( self , key1 , key2 , bond ) : self . graph . add_edge ( key1 , key2 , bond = bond )
11,865
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/model/graphmol.py#L100-L102
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Iterate over bonds .
def bonds_iter ( self ) : for u , v , bond in self . graph . edges . data ( "bond" ) : yield u , v , bond
11,866
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/model/graphmol.py#L108-L111
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Return dict of neighbor atom index and connecting bond .
def neighbors ( self , key ) : return { n : attr [ "bond" ] for n , attr in self . graph [ key ] . items ( ) }
11,867
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/model/graphmol.py#L121-L123
[ "def", "calc_regenerated", "(", "self", ",", "lastvotetime", ")", ":", "delta", "=", "datetime", ".", "utcnow", "(", ")", "-", "datetime", ".", "strptime", "(", "lastvotetime", ",", "'%Y-%m-%dT%H:%M:%S'", ")", "td", "=", "delta", ".", "days", "ts", "=", "delta", ".", "seconds", "tt", "=", "(", "td", "*", "86400", ")", "+", "ts", "return", "tt", "*", "10000", "/", "86400", "/", "5" ]
Iterate over atoms and return its neighbors .
def neighbors_iter ( self ) : for n , adj in self . graph . adj . items ( ) : yield n , { n : attr [ "bond" ] for n , attr in adj . items ( ) }
11,868
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/model/graphmol.py#L129-L132
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Empty the instance
def clear ( self ) : # self.graph = nx.Graph() self . graph . clear ( ) self . data . clear ( ) self . descriptors . clear ( ) self . size2d = None self . rings = None self . scaffolds = None self . isolated = None
11,869
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/model/graphmol.py#L134-L143
[ "def", "search_for_port", "(", "port_glob", ",", "req", ",", "expected_res", ")", ":", "# Check that the USB port actually exists, based on the known vendor and", "# product ID.", "if", "usb", ".", "core", ".", "find", "(", "idVendor", "=", "0x0403", ",", "idProduct", "=", "0x6001", ")", "is", "None", ":", "return", "None", "# Find ports matching the supplied glob.", "ports", "=", "glob", ".", "glob", "(", "port_glob", ")", "if", "len", "(", "ports", ")", "==", "0", ":", "return", "None", "for", "port", "in", "ports", ":", "with", "r12_serial_port", "(", "port", ")", "as", "ser", ":", "if", "not", "ser", ".", "isOpen", "(", ")", ":", "ser", ".", "open", "(", ")", "# Write a request out.", "if", "sys", ".", "version_info", "[", "0", "]", "==", "2", ":", "ser", ".", "write", "(", "str", "(", "req", ")", ".", "encode", "(", "'utf-8'", ")", ")", "else", ":", "ser", ".", "write", "(", "bytes", "(", "req", ",", "'utf-8'", ")", ")", "# Wait a short period to allow the connection to generate output.", "time", ".", "sleep", "(", "0.1", ")", "# Read output from the serial connection check if it's what we want.", "res", "=", "ser", ".", "read", "(", "ser", ".", "in_waiting", ")", ".", "decode", "(", "OUTPUT_ENCODING", ")", "if", "expected_res", "in", "res", ":", "return", "port", "raise", "ArmException", "(", "'ST Robotics connection found, but is not responsive.'", "+", "' Is the arm powered on?'", ")", "return", "None" ]
For QPainter coordinate system reflect over X axis and translate from center to top - left
def _convert ( self , pos ) : px = pos [ 0 ] + self . logical_size . width ( ) / 2 py = self . logical_size . height ( ) / 2 - pos [ 1 ] return px , py
11,870
https://github.com/mojaie/chorus/blob/fc7fe23a0272554c67671645ab07830b315eeb1b/chorus/draw/qt.py#L181-L187
[ "async", "def", "async_get_bridgeid", "(", "session", ",", "host", ",", "port", ",", "api_key", ",", "*", "*", "kwargs", ")", ":", "url", "=", "'http://{}:{}/api/{}/config'", ".", "format", "(", "host", ",", "str", "(", "port", ")", ",", "api_key", ")", "response", "=", "await", "async_request", "(", "session", ".", "get", ",", "url", ")", "bridgeid", "=", "response", "[", "'bridgeid'", "]", "_LOGGER", ".", "info", "(", "\"Bridge id: %s\"", ",", "bridgeid", ")", "return", "bridgeid" ]
Run the Sphinx build process .
def run_sphinx ( root_dir ) : logger = logging . getLogger ( __name__ ) # This replicates what Sphinx's internal command line hander does in # https://github.com/sphinx-doc/sphinx/blob/master/sphinx/cmd/build.py # build_main() # configuration root_dir = os . path . abspath ( root_dir ) srcdir = root_dir # root directory of Sphinx content confdir = root_dir # directory where conf.py is located outdir = os . path . join ( root_dir , '_build' , 'html' ) doctreedir = os . path . join ( root_dir , '_build' , 'doctree' ) builder = 'html' confoverrides = { } status = sys . stdout # set to None for 'quiet' mode warning = sys . stderr error = sys . stderr freshenv = False # attempt to re-use existing build artificats warningiserror = False tags = [ ] verbosity = 0 jobs = 1 # number of processes force_all = True filenames = [ ] logger . debug ( 'Sphinx config: srcdir={0}' . format ( srcdir ) ) logger . debug ( 'Sphinx config: confdir={0}' . format ( confdir ) ) logger . debug ( 'Sphinx config: outdir={0}' . format ( outdir ) ) logger . debug ( 'Sphinx config: doctreedir={0}' . format ( doctreedir ) ) logger . debug ( 'Sphinx config: builder={0}' . format ( builder ) ) logger . debug ( 'Sphinx config: freshenv={0:b}' . format ( freshenv ) ) logger . debug ( 'Sphinx config: warningiserror={0:b}' . format ( warningiserror ) ) logger . debug ( 'Sphinx config: verbosity={0:d}' . format ( verbosity ) ) logger . debug ( 'Sphinx config: jobs={0:d}' . format ( jobs ) ) logger . debug ( 'Sphinx config: force_all={0:b}' . format ( force_all ) ) app = None try : with patch_docutils ( ) , docutils_namespace ( ) : app = Sphinx ( srcdir , confdir , outdir , doctreedir , builder , confoverrides , status , warning , freshenv , warningiserror , tags , verbosity , jobs ) app . build ( force_all , filenames ) return app . statuscode except ( Exception , KeyboardInterrupt ) as exc : args = MockSphinxNamespace ( verbosity = verbosity , traceback = True ) handle_exception ( app , args , exc , error ) return 1
11,871
https://github.com/lsst-sqre/documenteer/blob/75f02901a80042b28d074df1cc1dca32eb8e38c8/documenteer/sphinxrunner.py#L19-L90
[ "def", "_ensure_file_path", "(", "self", ")", ":", "storage_root", "=", "os", ".", "path", ".", "dirname", "(", "self", ".", "file_path", ")", "needs_storage_root", "=", "storage_root", "and", "not", "os", ".", "path", ".", "isdir", "(", "storage_root", ")", "if", "needs_storage_root", ":", "# pragma: no cover", "os", ".", "makedirs", "(", "storage_root", ")", "if", "not", "os", ".", "path", ".", "isfile", "(", "self", ".", "file_path", ")", ":", "# create the file without group/world permissions", "with", "open", "(", "self", ".", "file_path", ",", "'w'", ")", ":", "pass", "user_read_write", "=", "0o600", "os", ".", "chmod", "(", "self", ".", "file_path", ",", "user_read_write", ")" ]
Search and load a configuration file .
def get_settings ( config_file ) : default_settings = { 'general' : { 'endpoint' : 'http://guacamole.antojitos.io/files/' , 'shortener' : 'http://t.antojitos.io/api/v1/urls' , } } settings = configparser . ConfigParser ( ) try : settings . read_dict ( default_settings ) except AttributeError : # using python 2.7 for section , options in default_settings . items ( ) : settings . add_section ( section ) for option , value in options . items ( ) : settings . set ( section , option , value ) if config_file is not None and os . path . exists ( config_file ) : settings . read ( config_file ) return settings if os . path . exists ( CONFIG_FILE ) : settings . read ( CONFIG_FILE ) return settings return settings
11,872
https://github.com/Antojitos/guacamole-cli/blob/e3ae6b8eb08379ffb784978587bf24b168af73d0/src/guacamole_cli/__init__.py#L16-L41
[ "def", "delete_selection", "(", "self", ")", ":", "selection", "=", "self", ".", "selection", "if", "selection", "is", "None", ":", "return", "if", "isinstance", "(", "selection", ",", "ArrowWidget", ")", ":", "self", ".", "mainscreen", ".", "boardview", ".", "board", ".", "rm_arrow", "(", "selection", ".", "origin", ".", "name", ",", "selection", ".", "destination", ".", "name", ")", "selection", ".", "portal", ".", "delete", "(", ")", "elif", "isinstance", "(", "selection", ",", "Spot", ")", ":", "self", ".", "mainscreen", ".", "boardview", ".", "board", ".", "rm_spot", "(", "selection", ".", "name", ")", "selection", ".", "proxy", ".", "delete", "(", ")", "else", ":", "assert", "isinstance", "(", "selection", ",", "Pawn", ")", "self", ".", "mainscreen", ".", "boardview", ".", "board", ".", "rm_pawn", "(", "selection", ".", "name", ")", "selection", ".", "proxy", ".", "delete", "(", ")", "self", ".", "selection", "=", "None" ]
Encrypts a string using a given rsa . PublicKey object . If the message is larger than the key it will split it up into a list and encrypt each line in the list .
def encrypt ( self , message , public_key ) : # Get the maximum message length based on the key max_str_len = rsa . common . byte_size ( public_key . n ) - 11 # If the message is longer than the key size, split it into a list to # be encrypted if len ( message ) > max_str_len : message = textwrap . wrap ( message , width = max_str_len ) else : message = [ message ] # Create a list for the encrypted message to send enc_msg = [ ] # If we have a long message, loop through and encrypt each part of the # string for line in message : # Encrypt the line in the message into a bytestring enc_line = rsa . encrypt ( line , public_key ) # Convert the encrypted bytestring into ASCII, so we can send it # over the network enc_line_converted = binascii . b2a_base64 ( enc_line ) enc_msg . append ( enc_line_converted ) # Serialize the encrypted message again with json enc_msg = json . dumps ( enc_msg ) # Return the list of encrypted strings return enc_msg
11,873
https://github.com/ShadowBlip/Neteria/blob/1a8c976eb2beeca0a5a272a34ac58b2c114495a4/neteria/encryption.py#L43-L87
[ "def", "setOverlayTextureColorSpace", "(", "self", ",", "ulOverlayHandle", ",", "eTextureColorSpace", ")", ":", "fn", "=", "self", ".", "function_table", ".", "setOverlayTextureColorSpace", "result", "=", "fn", "(", "ulOverlayHandle", ",", "eTextureColorSpace", ")", "return", "result" ]
Decrypts a string using our own private key object .
def decrypt ( self , message ) : # Unserialize the encrypted message message = json . loads ( message ) # Set up a list for the unencrypted lines of the message unencrypted_msg = [ ] for line in message : # Convert from ascii back to bytestring enc_line = binascii . a2b_base64 ( line ) # Decrypt the line using our private key unencrypted_line = rsa . decrypt ( enc_line , self . private_key ) unencrypted_msg . append ( unencrypted_line ) # Convert the message from a list back into a string unencrypted_msg = "" . join ( unencrypted_msg ) return unencrypted_msg
11,874
https://github.com/ShadowBlip/Neteria/blob/1a8c976eb2beeca0a5a272a34ac58b2c114495a4/neteria/encryption.py#L90-L120
[ "def", "gumbel_sample", "(", "shape", ")", ":", "uniform_samples", "=", "tf", ".", "random_uniform", "(", "shape", ",", "minval", "=", "0.00001", ",", "maxval", "=", "0.99998", ")", "return", "-", "tf", ".", "log", "(", "-", "tf", ".", "log", "(", "uniform_samples", ")", ")" ]
On any event method
def on_any_event ( self , event ) : for delegate in self . delegates : if hasattr ( delegate , "on_any_event" ) : delegate . on_any_event ( event )
11,875
https://github.com/mastro35/flows/blob/05e488385673a69597b5b39c7728795aa4d5eb18/flows/Actions/InputWatchdogAction.py#L28-L32
[ "def", "from_manifest", "(", "app", ",", "filename", ",", "raw", "=", "False", ",", "*", "*", "kwargs", ")", ":", "cfg", "=", "current_app", ".", "config", "if", "current_app", ".", "config", ".", "get", "(", "'TESTING'", ")", ":", "return", "# Do not spend time here when testing", "path", "=", "_manifests", "[", "app", "]", "[", "filename", "]", "if", "not", "raw", "and", "cfg", ".", "get", "(", "'CDN_DOMAIN'", ")", "and", "not", "cfg", ".", "get", "(", "'CDN_DEBUG'", ")", ":", "scheme", "=", "'https'", "if", "cfg", ".", "get", "(", "'CDN_HTTPS'", ")", "else", "request", ".", "scheme", "prefix", "=", "'{}://'", ".", "format", "(", "scheme", ")", "if", "not", "path", ".", "startswith", "(", "'/'", ")", ":", "# CDN_DOMAIN has no trailing slash", "path", "=", "'/'", "+", "path", "return", "''", ".", "join", "(", "(", "prefix", ",", "cfg", "[", "'CDN_DOMAIN'", "]", ",", "path", ")", ")", "elif", "not", "raw", "and", "kwargs", ".", "get", "(", "'external'", ",", "False", ")", ":", "if", "path", ".", "startswith", "(", "'/'", ")", ":", "# request.host_url has a trailing slash", "path", "=", "path", "[", "1", ":", "]", "return", "''", ".", "join", "(", "(", "request", ".", "host_url", ",", "path", ")", ")", "return", "path" ]
On created method
def on_created ( self , event ) : for delegate in self . delegates : if hasattr ( delegate , "on_created" ) : delegate . on_created ( event )
11,876
https://github.com/mastro35/flows/blob/05e488385673a69597b5b39c7728795aa4d5eb18/flows/Actions/InputWatchdogAction.py#L34-L38
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On deleted method
def on_deleted ( self , event ) : for delegate in self . delegates : if hasattr ( delegate , "on_deleted" ) : delegate . on_deleted ( event )
11,877
https://github.com/mastro35/flows/blob/05e488385673a69597b5b39c7728795aa4d5eb18/flows/Actions/InputWatchdogAction.py#L40-L44
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On modified method
def on_modified ( self , event ) : for delegate in self . delegates : if hasattr ( delegate , "on_modified" ) : delegate . on_modified ( event )
11,878
https://github.com/mastro35/flows/blob/05e488385673a69597b5b39c7728795aa4d5eb18/flows/Actions/InputWatchdogAction.py#L46-L50
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On moved method
def on_moved ( self , event ) : for delegate in self . delegates : if hasattr ( delegate , "on_moved" ) : delegate . on_moved ( event )
11,879
https://github.com/mastro35/flows/blob/05e488385673a69597b5b39c7728795aa4d5eb18/flows/Actions/InputWatchdogAction.py#L52-L56
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Fired when something s been created
def on_created ( self , event ) : if self . trigger != "create" : return action_input = ActionInput ( event , "" , self . name ) flows . Global . MESSAGE_DISPATCHER . send_message ( action_input )
11,880
https://github.com/mastro35/flows/blob/05e488385673a69597b5b39c7728795aa4d5eb18/flows/Actions/InputWatchdogAction.py#L118-L123
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Start background thread if not already started
def start ( cls ) : if cls . _thread is None : cls . _thread = threading . Thread ( target = cls . _run , name = "Heartbeat" ) cls . _thread . daemon = True cls . _thread . start ( )
11,881
https://github.com/zsimic/runez/blob/14363b719a1aae1528859a501a22d075ce0abfcc/src/runez/heartbeat.py#L82-L87
[ "def", "GetAttachmentIdFromMediaId", "(", "media_id", ")", ":", "altchars", "=", "'+-'", "if", "not", "six", ".", "PY2", ":", "altchars", "=", "altchars", ".", "encode", "(", "'utf-8'", ")", "# altchars for '+' and '/'. We keep '+' but replace '/' with '-'", "buffer", "=", "base64", ".", "b64decode", "(", "str", "(", "media_id", ")", ",", "altchars", ")", "resoure_id_length", "=", "20", "attachment_id", "=", "''", "if", "len", "(", "buffer", ")", ">", "resoure_id_length", ":", "# We are cutting off the storage index.", "attachment_id", "=", "base64", ".", "b64encode", "(", "buffer", "[", "0", ":", "resoure_id_length", "]", ",", "altchars", ")", "if", "not", "six", ".", "PY2", ":", "attachment_id", "=", "attachment_id", ".", "decode", "(", "'utf-8'", ")", "else", ":", "attachment_id", "=", "media_id", "return", "attachment_id" ]
Task instance representing task if any
def resolved_task ( cls , task ) : for t in cls . tasks : if t is task or t . execute is task : return t
11,882
https://github.com/zsimic/runez/blob/14363b719a1aae1528859a501a22d075ce0abfcc/src/runez/heartbeat.py#L118-L122
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Background thread s main function execute registered tasks accordingly to their frequencies
def _run ( cls ) : if cls . _thread : with cls . _lock : # First run: execute each task once to get it started for task in cls . tasks : cls . _execute_task ( task ) cls . tasks . sort ( ) cls . _last_execution = time . time ( ) while cls . _thread : with cls . _lock : if cls . tasks : for task in cls . tasks : if task . next_execution - cls . _last_execution < 0.5 : cls . _execute_task ( task ) else : break cls . tasks . sort ( ) cls . _last_execution = time . time ( ) cls . _sleep_delay = cls . tasks [ 0 ] . next_execution - cls . _last_execution else : cls . _sleep_delay = 1 sleep_delay = max ( 0.1 , cls . _sleep_delay ) # Don't hold cls._lock while sleeping, sleep delay should be 1 second when no tasks are present time . sleep ( sleep_delay )
11,883
https://github.com/zsimic/runez/blob/14363b719a1aae1528859a501a22d075ce0abfcc/src/runez/heartbeat.py#L149-L177
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A standard method of creating parity plots between predicted and experimental values for trained models .
def parity_plot ( X , Y , model , devmodel , axes_labels = None ) : model_outputs = Y . shape [ 1 ] with plt . style . context ( 'seaborn-whitegrid' ) : fig = plt . figure ( figsize = ( 2.5 * model_outputs , 2.5 ) , dpi = 300 ) for i in range ( model_outputs ) : ax = fig . add_subplot ( 1 , model_outputs , i + 1 ) minval = np . min ( [ np . exp ( model . predict ( X ) [ : , i ] ) , np . exp ( Y ) [ : , i ] ] ) maxval = np . max ( [ np . exp ( model . predict ( X ) [ : , i ] ) , np . exp ( Y ) [ : , i ] ] ) buffer = ( maxval - minval ) / 100 * 2 minval = minval - buffer maxval = maxval + buffer ax . plot ( [ minval , maxval ] , [ minval , maxval ] , linestyle = "-" , label = None , c = "black" , linewidth = 1 ) ax . plot ( np . exp ( Y ) [ : , i ] , np . exp ( model . predict ( X ) ) [ : , i ] , marker = "*" , linestyle = "" , alpha = 0.4 ) if axes_labels : ax . set_ylabel ( "Predicted {}" . format ( axes_labels [ '{}' . format ( i ) ] ) ) ax . set_xlabel ( "Actual {}" . format ( axes_labels [ '{}' . format ( i ) ] ) ) else : ax . set_ylabel ( "Predicted {}" . format ( devmodel . Data . columns [ - ( 6 - i ) ] . split ( "<" ) [ 0 ] ) , wrap = True , fontsize = 5 ) ax . set_xlabel ( "Actual {}" . format ( devmodel . Data . columns [ - ( 6 - i ) ] . split ( "<" ) [ 0 ] ) , wrap = True , fontsize = 5 ) plt . xlim ( minval , maxval ) plt . ylim ( minval , maxval ) ax . grid ( ) plt . tight_layout ( ) return plt
11,884
https://github.com/wesleybeckner/salty/blob/ef17a97aea3e4f81fcd0359ce85b3438c0e6499b/salty/visualization.py#L6-L60
[ "def", "getADSLInfo", "(", "self", ",", "wanInterfaceId", "=", "1", ",", "timeout", "=", "1", ")", ":", "namespace", "=", "Wan", ".", "getServiceType", "(", "\"getADSLInfo\"", ")", "+", "str", "(", "wanInterfaceId", ")", "uri", "=", "self", ".", "getControlURL", "(", "namespace", ")", "results", "=", "self", ".", "execute", "(", "uri", ",", "namespace", ",", "\"GetInfo\"", ",", "timeout", "=", "timeout", ")", "return", "ADSLInfo", "(", "results", ")" ]
generate year month day features from specified date features
def expand_dates ( df , columns = [ ] ) : columns = df . columns . intersection ( columns ) df2 = df . reindex ( columns = set ( df . columns ) . difference ( columns ) ) for column in columns : df2 [ column + '_year' ] = df [ column ] . apply ( lambda x : x . year ) df2 [ column + '_month' ] = df [ column ] . apply ( lambda x : x . month ) df2 [ column + '_day' ] = df [ column ] . apply ( lambda x : x . day ) return df2
11,885
https://github.com/potash/drain/blob/ddd62081cb9317beb5d21f86c8b4bb196ca3d222/drain/data.py#L203-L213
[ "def", "get_connection_details", "(", "session", ",", "vcenter_resource_model", ",", "resource_context", ")", ":", "session", "=", "session", "resource_context", "=", "resource_context", "# get vCenter connection details from vCenter resource", "user", "=", "vcenter_resource_model", ".", "user", "vcenter_url", "=", "resource_context", ".", "address", "password", "=", "session", ".", "DecryptPassword", "(", "vcenter_resource_model", ".", "password", ")", ".", "Value", "return", "VCenterConnectionDetails", "(", "vcenter_url", ",", "user", ",", "password", ")" ]
Binarize specified categoricals . Works inplace!
def binarize ( df , category_classes , all_classes = True , drop = True , astype = None , inplace = True , min_freq = None ) : if type ( category_classes ) is not dict : columns = set ( category_classes ) category_classes = { column : df [ column ] . unique ( ) for column in columns } else : columns = category_classes . keys ( ) df_new = df if inplace else df . drop ( columns , axis = 1 ) for category in columns : classes = category_classes [ category ] for i in range ( len ( classes ) - 1 if not all_classes else len ( classes ) ) : c = df [ category ] == classes [ i ] if not min_freq or c . sum ( ) >= min_freq : if astype is not None : c = c . astype ( astype ) df_new [ '%s_%s' % ( category , str ( classes [ i ] ) . replace ( ' ' , '_' ) ) ] = c if drop and inplace : df_new . drop ( columns , axis = 1 , inplace = True ) return df_new
11,886
https://github.com/potash/drain/blob/ddd62081cb9317beb5d21f86c8b4bb196ca3d222/drain/data.py#L216-L255
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select subset of strings matching a regex treats strings as a set
def select_regexes ( strings , regexes ) : strings = set ( strings ) select = set ( ) if isinstance ( strings , collections . Iterable ) : for r in regexes : s = set ( filter ( re . compile ( '^' + r + '$' ) . search , strings ) ) strings -= s select |= s return select else : raise ValueError ( "exclude should be iterable" )
11,887
https://github.com/potash/drain/blob/ddd62081cb9317beb5d21f86c8b4bb196ca3d222/drain/data.py#L399-L413
[ "def", "get_status", "(", "self", ")", ":", "status", "=", "ctypes", ".", "c_int32", "(", ")", "result", "=", "self", ".", "library", ".", "Par_GetStatus", "(", "self", ".", "pointer", ",", "ctypes", ".", "byref", "(", "status", ")", ")", "check_error", "(", "result", ",", "\"partner\"", ")", "return", "status" ]
parse a string to a delta all is represented by None
def parse_delta ( s ) : if s == 'all' : return None else : ls = delta_regex . findall ( s ) if len ( ls ) == 1 : return relativedelta ( * * { delta_chars [ ls [ 0 ] [ 1 ] ] : int ( ls [ 0 ] [ 0 ] ) } ) else : raise ValueError ( 'Invalid delta string: %s' % s )
11,888
https://github.com/potash/drain/blob/ddd62081cb9317beb5d21f86c8b4bb196ca3d222/drain/data.py#L623-L635
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Takes a pd . DataFrame and returns the newly defined column i . e . a pd . Series that has the same index as df .
def apply ( self , df ) : if hasattr ( self . definition , '__call__' ) : r = self . definition ( df ) elif self . definition in df . columns : r = df [ self . definition ] elif not isinstance ( self . definition , string_types ) : r = pd . Series ( self . definition , index = df . index ) else : raise ValueError ( "Invalid column definition: %s" % str ( self . definition ) ) return r . astype ( self . astype ) if self . astype else r
11,889
https://github.com/potash/drain/blob/ddd62081cb9317beb5d21f86c8b4bb196ca3d222/drain/data.py#L44-L56
[ "def", "delete_all_volumes", "(", "self", ")", ":", "# Raise an exception if we are not a manager", "if", "not", "self", ".", "_manager", ":", "raise", "RuntimeError", "(", "'Volumes can only be deleted '", "'on swarm manager nodes'", ")", "volume_list", "=", "self", ".", "get_volume_list", "(", ")", "for", "volumes", "in", "volume_list", ":", "# Remove all the services", "self", ".", "_api_client", ".", "remove_volume", "(", "volumes", ",", "force", "=", "True", ")" ]
Convert ip address to a network byte order 32 - bit integer .
def ip_to_long ( ip ) : quad = ip . split ( '.' ) if len ( quad ) == 1 : quad = quad + [ 0 , 0 , 0 ] elif len ( quad ) < 4 : host = quad [ - 1 : ] quad = quad [ : - 1 ] + [ 0 , ] * ( 4 - len ( quad ) ) + host lip = 0 for q in quad : lip = ( lip << 8 ) | int ( q ) return lip
11,890
https://github.com/untwisted/untwisted/blob/8a8d9c8a8d0f3452d5de67cd760297bb5759f637/untwisted/iputils.py#L1-L15
[ "def", "snapshot_agents", "(", "self", ",", "force", "=", "False", ")", ":", "for", "agent", "in", "self", ".", "_agents", ":", "agent", ".", "check_if_should_snapshot", "(", "force", ")" ]
Link to LSST documents given their handle using LSST s ls . st link shortener .
def lsst_doc_shortlink_role ( name , rawtext , text , lineno , inliner , options = None , content = None ) : options = options or { } content = content or [ ] node = nodes . reference ( text = '{0}-{1}' . format ( name . upper ( ) , text ) , refuri = 'https://ls.st/{0}-{1}' . format ( name , text ) , * * options ) return [ node ] , [ ]
11,891
https://github.com/lsst-sqre/documenteer/blob/75f02901a80042b28d074df1cc1dca32eb8e38c8/documenteer/sphinxext/lsstdocushare.py#L6-L21
[ "def", "update_config", "(", "self", ",", "config_dict", ",", "config_file", ")", ":", "config_path", "=", "path", ".", "dirname", "(", "config_file", ")", "self", ".", "config", ".", "config_file_path", "=", "config_file", "self", ".", "config", ".", "path", "=", "config_path", "for", "config_key", ",", "config_value", "in", "config_dict", ".", "items", "(", ")", ":", "if", "config_value", "!=", "self", ".", "config", ".", "get_config_value", "(", "config_key", ")", ":", "self", ".", "set_preliminary_config_value", "(", "config_key", ",", "config_value", ")" ]
Link to LSST documents given their handle using LSST s ls . st link shortener with the document handle displayed in title case .
def lsst_doc_shortlink_titlecase_display_role ( name , rawtext , text , lineno , inliner , options = None , content = None ) : options = options or { } content = content or [ ] node = nodes . reference ( text = '{0}-{1}' . format ( name . title ( ) , text ) , refuri = 'https://ls.st/{0}-{1}' . format ( name , text ) , * * options ) return [ node ] , [ ]
11,892
https://github.com/lsst-sqre/documenteer/blob/75f02901a80042b28d074df1cc1dca32eb8e38c8/documenteer/sphinxext/lsstdocushare.py#L24-L42
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Command line entrypoint for the refresh - lsst - bib program .
def run ( ) : args = parse_args ( ) if args . verbose : log_level = logging . DEBUG else : log_level = logging . INFO logging . basicConfig ( level = log_level , format = '%(asctime)s %(levelname)s %(name)s: %(message)s' ) if not args . verbose : # Manage third-party loggers req_logger = logging . getLogger ( 'requests' ) req_logger . setLevel ( logging . WARNING ) logger = logging . getLogger ( __name__ ) logger . info ( 'refresh-lsst-bib version {}' . format ( __version__ ) ) error_count = process_bib_files ( args . dir ) sys . exit ( error_count )
11,893
https://github.com/lsst-sqre/documenteer/blob/75f02901a80042b28d074df1cc1dca32eb8e38c8/documenteer/bin/refreshlsstbib.py#L20-L43
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Command line entrypoint for the build - stack - docs program .
def run_build_cli ( ) : args = parse_args ( ) if args . verbose : log_level = logging . DEBUG else : log_level = logging . INFO logging . basicConfig ( level = log_level , format = '%(asctime)s %(levelname)s %(name)s: %(message)s' ) logger = logging . getLogger ( __name__ ) logger . info ( 'build-stack-docs version {0}' . format ( __version__ ) ) return_code = build_stack_docs ( args . root_project_dir ) if return_code == 0 : logger . info ( 'build-stack-docs succeeded' ) sys . exit ( 0 ) else : logger . error ( 'Sphinx errored: code {0:d}' . format ( return_code ) ) sys . exit ( 1 )
11,894
https://github.com/lsst-sqre/documenteer/blob/75f02901a80042b28d074df1cc1dca32eb8e38c8/documenteer/stackdocs/build.py#L25-L48
[ "def", "update", "(", "self", ",", "other", ")", ":", "self", ".", "update_ttl", "(", "other", ".", "ttl", ")", "super", "(", "Rdataset", ",", "self", ")", ".", "update", "(", "other", ")" ]
Create an argument parser for the build - stack - docs program .
def parse_args ( ) : parser = argparse . ArgumentParser ( description = "Build a Sphinx documentation site for an EUPS stack, " "such as pipelines.lsst.io." , epilog = "Version {0}" . format ( __version__ ) ) parser . add_argument ( '-d' , '--dir' , dest = 'root_project_dir' , help = "Root Sphinx project directory" ) parser . add_argument ( '-v' , '--verbose' , dest = 'verbose' , action = 'store_true' , default = False , help = 'Enable Verbose output (debug level logging)' ) return parser . parse_args ( )
11,895
https://github.com/lsst-sqre/documenteer/blob/75f02901a80042b28d074df1cc1dca32eb8e38c8/documenteer/stackdocs/build.py#L133-L156
[ "def", "getVATAmount", "(", "self", ")", ":", "price", ",", "vat", "=", "self", ".", "getPrice", "(", ")", ",", "self", ".", "getVAT", "(", ")", "return", "float", "(", "price", ")", "*", "(", "float", "(", "vat", ")", "/", "100", ")" ]
Summarize packages currently set up by EUPS listing their set up directories and EUPS version names .
def discover_setup_packages ( ) : logger = logging . getLogger ( __name__ ) # Not a PyPI dependency; assumed to be available in the build environment. import eups eups_client = eups . Eups ( ) products = eups_client . getSetupProducts ( ) packages = { } for package in products : name = package . name info = { 'dir' : package . dir , 'version' : package . version } packages [ name ] = info logger . debug ( 'Found setup package: {name} {version} {dir}' . format ( name = name , * * info ) ) return packages
11,896
https://github.com/lsst-sqre/documenteer/blob/75f02901a80042b28d074df1cc1dca32eb8e38c8/documenteer/stackdocs/build.py#L159-L198
[ "def", "removeAll", "(", "self", ")", ":", "rv", "=", "self", ".", "_removeAll", "(", "self", ".", "_reads", ",", "self", ".", "_writes", ")", "return", "rv" ]
Find the EUPS table file for a project .
def find_table_file ( root_project_dir ) : ups_dir_path = os . path . join ( root_project_dir , 'ups' ) table_path = None for name in os . listdir ( ups_dir_path ) : if name . endswith ( '.table' ) : table_path = os . path . join ( ups_dir_path , name ) break if not os . path . exists ( table_path ) : raise RuntimeError ( 'Could not find the EUPS table file at {}' . format ( table_path ) ) return table_path
11,897
https://github.com/lsst-sqre/documenteer/blob/75f02901a80042b28d074df1cc1dca32eb8e38c8/documenteer/stackdocs/build.py#L201-L225
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List the names of packages that are required by an EUPS table file .
def list_packages_in_eups_table ( table_text ) : logger = logging . getLogger ( __name__ ) # This pattern matches required product names in EUPS table files. pattern = re . compile ( r'setupRequired\((?P<name>\w+)\)' ) listed_packages = [ m . group ( 'name' ) for m in pattern . finditer ( table_text ) ] logger . debug ( 'Packages listed in the table file: %r' , listed_packages ) return listed_packages
11,898
https://github.com/lsst-sqre/documenteer/blob/75f02901a80042b28d074df1cc1dca32eb8e38c8/documenteer/stackdocs/build.py#L228-L246
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Find documentation directories in a package using manifest . yaml .
def find_package_docs ( package_dir , skippedNames = None ) : logger = logging . getLogger ( __name__ ) if skippedNames is None : skippedNames = [ ] doc_dir = os . path . join ( package_dir , 'doc' ) modules_yaml_path = os . path . join ( doc_dir , 'manifest.yaml' ) if not os . path . exists ( modules_yaml_path ) : raise NoPackageDocs ( 'Manifest YAML not found: {0}' . format ( modules_yaml_path ) ) with open ( modules_yaml_path ) as f : manifest_data = yaml . safe_load ( f ) module_dirs = { } package_dirs = { } static_dirs = { } if 'modules' in manifest_data : for module_name in manifest_data [ 'modules' ] : if module_name in skippedNames : logger . debug ( 'Skipping module {0}' . format ( module_name ) ) continue module_dir = os . path . join ( doc_dir , module_name ) # validate that the module's documentation directory does exist if not os . path . isdir ( module_dir ) : message = 'module doc dir not found: {0}' . format ( module_dir ) logger . warning ( message ) continue module_dirs [ module_name ] = module_dir logger . debug ( 'Found module doc dir {0}' . format ( module_dir ) ) if 'package' in manifest_data : package_name = manifest_data [ 'package' ] full_package_dir = os . path . join ( doc_dir , package_name ) # validate the directory exists if os . path . isdir ( full_package_dir ) and package_name not in skippedNames : package_dirs [ package_name ] = full_package_dir logger . debug ( 'Found package doc dir {0}' . format ( full_package_dir ) ) else : logger . warning ( 'package doc dir excluded or not found: {0}' . format ( full_package_dir ) ) if 'statics' in manifest_data : for static_dirname in manifest_data [ 'statics' ] : full_static_dir = os . path . join ( doc_dir , static_dirname ) # validate the directory exists if not os . path . isdir ( full_static_dir ) : message = '_static doc dir not found: {0}' . format ( full_static_dir ) logger . warning ( message ) continue # Make a relative path to `_static` that's used as the # link source in the root docproject's _static/ directory relative_static_dir = os . path . relpath ( full_static_dir , os . path . join ( doc_dir , '_static' ) ) static_dirs [ relative_static_dir ] = full_static_dir logger . debug ( 'Found _static doc dir: {0}' . format ( full_static_dir ) ) Dirs = namedtuple ( 'Dirs' , [ 'module_dirs' , 'package_dirs' , 'static_dirs' ] ) return Dirs ( module_dirs = module_dirs , package_dirs = package_dirs , static_dirs = static_dirs )
11,899
https://github.com/lsst-sqre/documenteer/blob/75f02901a80042b28d074df1cc1dca32eb8e38c8/documenteer/stackdocs/build.py#L249-L395
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