biomodels.runner¶

Runner producing a SuiteResult from a BioModels selection.

The pipeline itself (sbml2cellml.testsuite.runner.run_suite) is reused unchanged; this module only turns a list of model ids into runnable cases, skipping the ids whose info or download request fails, whose case cannot be built or whose model has no variable (prepare_cases), and runs them (run_biomodels).

prepare_cases ¶

prepare_cases(ids, cache=None)

Build the runnable cases of a list of BioModels ids.

Parameters:

Name	Type	Description	Default
`ids`	`list[str]`	BioModels ids, e.g. `BIOMD0000000001`.	required
`cache`	`Path \| None`	cache root, `sbml2cellml.testsuite.cases.cache_dir()` by default.	`None`

Returns:

Type	Description
`list[Case]`	The cases built and a skip reason per id whose info or download
`dict[str, str]`	request failed (`download failed: <ExceptionType>`), whose case
`tuple[list[Case], dict[str, str]]`	could not be built (`case failed: <ExceptionType>`) or whose model
`tuple[list[Case], dict[str, str]]`	has no variable (`no variables`); a case with SBML packages is still
`tuple[list[Case], dict[str, str]]`	returned, `sbml2cellml.testsuite.cases.skip_reason` skips it later.

run_biomodels ¶

run_biomodels(
    ids,
    cache=None,
    work_dir=Path("biomodels/work"),
    timeout=60.0,
    progress=None,
)

Run the pipeline for a list of BioModels ids.

Parameters:

Name	Type	Description	Default
`ids`	`list[str]`	BioModels ids to run.	required
`cache`	`Path \| None`	cache root, `sbml2cellml.testsuite.cases.cache_dir()` by default.	`None`
`work_dir`	`Path`	directory for the converted files, created if needed.	`Path('biomodels/work')`
`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, see `sbml2cellml.testsuite.runner.run_suite`.	`None`

Returns:

Type	Description
`SuiteResult`	The suite result, `suite="biomodels"`.