testsuite.simulators¶

Simulator functions run inside a SimulatorWorker.

Every function imports its simulator lazily, so a worker process loads only the simulator it is used for: roadrunner and libopencor bundle different LLVM versions and crash once both have compiled in the same process. Results are plain dictionaries (columns, rows) so they can be sent between processes.

simulate_sbml ¶

simulate_sbml(
    sbml,
    selections,
    start,
    end,
    steps,
    relative_tolerance=None,
    absolute_tolerance=None,
    maximum_number_of_steps=None,
)

Uniform timecourse of an SBML model with roadrunner.

Parameters:

Name	Type	Description	Default
`sbml`	`str`	SBML document as string.	required
`selections`	`list[str]`	roadrunner selections after `time`, e.g. `S1`, `[S1]`.	required
`start`	`float`	start time.	required
`end`	`float`	end time.	required
`steps`	`int`	number of intervals, the result has `steps + 1` rows.	required
`relative_tolerance`	`float \| None`	relative tolerance of the integrator, the roadrunner default when `None`.	`None`
`absolute_tolerance`	`float \| None`	absolute tolerance of the integrator, the roadrunner default when `None`.	`None`
`maximum_number_of_steps`	`int \| None`	internal steps of the integrator between two time points, the roadrunner default (20000) when `None`.	`None`

Returns:

Type	Description
`dict[str, Any]`	`columns` (the selections with `time` first) and `rows`.

simulate_cellml ¶

simulate_cellml(
    cellml_path,
    start,
    end,
    steps,
    relative_tolerance=None,
    absolute_tolerance=None,
    maximum_number_of_steps=None,
)

Uniform timecourse of a CellML model with libopencor.

Parameters:

Name	Type	Description	Default
`cellml_path`	`str`	path of the CellML file.	required
`start`	`float`	start time.	required
`end`	`float`	end time.	required
`steps`	`int`	number of intervals.	required
`relative_tolerance`	`float \| None`	relative tolerance of the ODE solver, the libopencor default when `None`.	`None`
`absolute_tolerance`	`float \| None`	absolute tolerance of the ODE solver, the libopencor default when `None`.	`None`
`maximum_number_of_steps`	`int \| None`	internal steps of the ODE solver between two time points, the default of `run_timecourse` when `None`.	`None`

Returns:

Type	Description
`dict[str, Any]`	`columns` (`time` first, then every variable) and `rows`.

sleep ¶

sleep(seconds)

Sleep, for the timeout tests of the worker.

Parameters:

Name	Type	Description	Default
`seconds`	`float`	how long.	required

Returns:

Type	Description
`dict[str, Any]`	`slept` with the seconds.