compspec package

Subpackages

• compspec.lp package
  • Module contents
• compspec.runner package
  • Submodules
  • compspec.runner.base module
  • compspec.runner.combination module
  • compspec.runner.composition module
  • compspec.runner.diff module
  • Module contents

Submodules

compspec.entity module

class compspec.entity. Counter ( prefix = 'id' )

Bases: object

A simple counter (iterator) that will yield the next number with some prefix.

compspec.entity. get_counter ( prefix = 'id' )

Return an iterable counter.

class compspec.entity. node ( nodeid , name , value , is_connector = False )

Bases: object

A node in a graph.

property args

describe ( )

to_dict ( )

class compspec.entity. relation ( fromid , toid , relation = 'has' )

Bases: object

A relation in a graph.

property args

to_dict ( )

compspec.graph module

class compspec.graph. Graph

Bases: object

A graph implicitly is scoped to one namespace

add_node ( node )

Add an already generated node.

add_relation ( relation )

Add an already generated relation.

classmethod from_dict ( obj )

Return a new graph loaded from a dictionary.

gen ( name , value , parent , nodeid = None , relation = 'has' , is_connector = False )

Generate a node and relation in one swoop! A parent is required.

iter_connectors ( )

Yield connector nodes only

iter_nodes ( )

Yield nodes. If a comparison is being done, a namespace needs to be added (e.g., node, namespace, * args)

iter_relations ( )

Yield relations in the same manner.

new_node ( name , value , nodeid = None , is_connector = False )

Generate a node with a name (type) and value

is_connector is a flag that indicates the node is included in the graph, but itself should not be assessed for add/change/remove.

new_relation ( fromid , relation , toid )

Generate a relation between parent (fromid) and child (toid). The relation here does not hard code a namespace, but it will be required to compare between two graphs.

next ( )

Return next id in the counter.

to_dict ( )

Output dictionary representation of nodes and relations.

class compspec.graph. GraphGroup

Bases: object

A graph group is intended to hold and yield named graphs.

extract ( )

compspec.logger module

class compspec.logger. ColorizingStreamHandler ( nocolor=False , stream=<_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'> , use_threads=False )

Bases: StreamHandler

BLACK = 0

BLUE = 4

BOLD_SEQ = '\x1b[1m'

COLOR_SEQ = '\x1b[%dm'

CYAN = 6

GREEN = 2

MAGENTA = 5

RED = 1

RESET_SEQ = '\x1b[0m'

WHITE = 7

YELLOW = 3

can_color_tty ( )

colors = {'CRITICAL': 1, 'DEBUG': 4, 'ERROR': 1, 'INFO': 2, 'WARNING': 3}

decorate ( record )

emit ( record )

Emit a record.

If a formatter is specified, it is used to format the record. The record is then written to the stream with a trailing newline. If exception information is present, it is formatted using traceback.print_exception and appended to the stream. If the stream has an ‘encoding’ attribute, it is used to determine how to do the output to the stream.

property is_tty

class compspec.logger. Logger

Bases: object

cleanup ( )

debug ( msg )

error ( msg )

exit ( msg , return_code = 1 )

handler ( msg )

info ( msg )

location ( msg )

progress ( done = None , total = None )

set_level ( level )

set_stream_handler ( stream_handler )

shellcmd ( msg )

text_handler ( msg )

The default snakemake log handler. Prints the output to the console. Args:

msg (dict): the log message dictionary

warning ( msg )

compspec.logger. setup_logger ( quiet = False , printshellcmds = False , nocolor = False , stdout = False , debug = False , use_threads = False , wms_monitor = None )

compspec.solver module

class compspec.solver. AspFunction ( name , args = None )

Bases: object

An asp function

symbol ( positive = True )

class compspec.solver. AspFunctionBuilder

Bases: object

class compspec.solver. PyclingoDriver ( cores = True , out = None , quiet = False )

Bases: object

comment ( msg )

devnull ( )

fact ( head )

ASP fact (a rule without a body).

h1 ( name )

h2 ( name )

newline ( )

set_verbosity ( out , quiet = False )

Set (or update) verbosity or output stream.

solve ( setup , nmodels = 0 , stats = False , logic_programs = None , facts_only = False )

Run the solver for a model and some number of logic programs

title ( name , char )

class compspec.solver. Result ( asp = None )

Bases: object

Result of an ASP solve.

compspec.solver. argify ( arg )

Convert an argument into a clingo one.

compspec.utils module

compspec.utils. normalize_key ( key )

A key needs to be all lowercase, ideally with no spaces, etc.

compspec.utils. read_file ( filename )

compspec.utils. read_json ( filename )

compspec.utils. read_yaml ( filepath )

compspec.utils. recursive_find ( base , pattern = '*.py' )

recursive find will yield python files in all directory levels below a base path.

Arguments:

• base (str) : the base directory to search

• pattern: a pattern to match, defaults to * .py

compspec.utils. row ( cols )

compspec.utils. run_command ( cmd , stream = False )

use subprocess to send a command to the terminal.

Parameters

cmd: the command to send

compspec.utils. write_json ( data , filename )

compspec.version module

Module contents