cobra.core.configuration#
Provide a global configuration object.
Classes#
Define a global configuration object. |
Module Contents#
- class cobra.core.configuration.Configuration(**kwargs)[source]#
Define a global configuration object.
The attributes of this singleton object are used as default values by cobra functions.
- solver#
The default solver for new models. The solver choices are the ones provided by optlang and depend on solvers installed in your environment.
- Type:
{“glpk”, “cplex”, “gurobi”, “glpk_exact”}
- lower_bound#
The standard lower bound for reversible reactions (default -1000).
- Type:
float, optional
- bounds#
The default reaction bounds for newly created reactions. The bounds are in the form of lower_bound, upper_bound (default -1000.0, 1000.0).
- Type:
tuple of floats
- processes#
A default number of processes to use where multiprocessing is possible. The default number corresponds to the number of available cores (hyperthreads) minus one.
- Type:
int > 0
- cache_directory#
A path where the model cache should reside if caching is desired. The default directory depends on the operating system.
- Type:
pathlib.Path or str, optional
- max_cache_size#
The allowed maximum size of the model cache in bytes (default 1 GB).
- Type:
int, optional
- cache_expiration#
The expiration time in seconds for the model cache if any (default None).
- Type:
int, optional
- _solver = None#
- tolerance = 1e-07#
- lower_bound = None#
- upper_bound = None#
- processes = None#
- _cache_directory = None#
- max_cache_size = 104857600#
- cache_expiration = None#
- property bounds: Tuple[numbers.Number | None, numbers.Number | None]#
Return the lower, upper reaction bound pair.
- Returns:
The lower and upper bounds for new reactions.
- Return type:
tuple of number and number or None and None
- property solver: types.ModuleType#
Return the optlang solver interface.
- property cache_directory: pathlib.Path#
Return the model cache directory.