testsuite.runner¶

The pipeline of the harness.

Every runnable case goes through five stages: the roadrunner simulation of the original SBML, the conversion to CellML, the libopencor simulation of the CellML, the conversion back to SBML and the roadrunner simulation of the roundtrip SBML. Every simulation is compared with the expected results of the case. The simulators run in worker processes, the conversions in this process.

roadrunner_selections ¶

roadrunner_selections(case, model)

Roadrunner selections of the settings variables of the original model.

A species expected as concentration is selected as [id], everything else by id.

run_case ¶

run_case(case, work_dir, roadrunner, libopencor)

Run the five stages of a case.

Parameters:

Name	Type	Description	Default
`case`	`Case`	a runnable case.	required
`work_dir`	`Path`	directory for the converted files.	required
`roadrunner`	`SimulatorWorker`	worker for the SBML simulations.	required
`libopencor`	`SimulatorWorker`	worker for the CellML simulation.	required

Returns:

Type	Description
`CaseResult`	The stage results; a stage whose input stage failed is `skip`. Every
`CaseResult`	stage is `fail` when the case itself cannot be set up (e.g. an
`CaseResult`	unparsable SBML file). When `case.expected` is `None`, the
`CaseResult`	`roadrunner` simulation of the original model becomes the expected
`CaseResult`	results for `libopencor` and `roundtrip` when it succeeds; when it
`CaseResult`	fails, those two stages are `skip` (`roadrunner failed`) instead of
`CaseResult`	running, and `roadrunner` itself has no `max_excess` (there is
`CaseResult`	nothing to compare it with). `CaseResult.informative` is
`CaseResult`	`sbml2cellml.testsuite.compare.is_informative` of the expected frame
`CaseResult`	(the case's expected results, or the `roadrunner` simulation once it
`CaseResult`	is known), `None` when there is no expected frame, i.e.
`CaseResult`	`case.expected` is `None` and the `roadrunner` stage failed.

run_suite ¶

run_suite(cases, work_dir, timeout=60.0, progress=None)

Run the pipeline for every runnable case.

Parameters:

Name	Type	Description	Default
`cases`	`list[Case]`	the cases; unrunnable ones are recorded as skipped.	required
`work_dir`	`Path`	directory for the converted files, created if needed.	required
`timeout`	`float`	seconds per simulator call.	`60.0`
`progress`	`Callable[[str], None] \| None`	called with the finished status line of the case after every runnable case, e.g. `00001 roadrunner=pass sbml2cellml=pass libopencor=fail cellml2sbml=pass roundtrip=fail`.	`None`

Returns:

Type	Description
`SuiteResult`	The suite result.