cobra.core.configuration

Provide a global configuration object.

Module Contents

Classes

Configuration

Define a global configuration object.

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[source]

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”}

tolerance

The default tolerance for the solver being used (default 1E-07).

Type

float, optional

lower_bound

The standard lower bound for reversible reactions (default -1000).

Type

float, optional

upper_bound

The standard upper bound for all reactions (default 1000).

Type

float, optional

bounds[source]

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[source]

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

property solver: types.ModuleType[source]

Return the optlang solver interface.

property bounds: Tuple[Optional[numbers.Number], Optional[numbers.Number]][source]

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 cache_directory: pathlib.Path[source]

Return the model cache directory.

_set_default_solver() None[source]

Set the default solver from a preferred order.

_set_default_processes() None[source]

Set the default number of processes.

_set_default_cache_directory() None[source]

Set the platform-dependent default cache directory.

__repr__() str[source]

Return a string representation of the current configuration values.

_repr_html_() str[source]

Return a rich HTML representation of the current configuration values.

Notes

This special method is used automatically in Jupyter notebooks to display a result from a cell.