biomodels.cli¶

The sbml2cellml-biomodels command.

sbml2cellml-biomodels run [--models biomodels/models.json] [--ids ID,ID]
                          [--count N] [--work-dir biomodels/work]
                          [--results FILE] [--report FILE] [--timeout SECONDS] [-v]
sbml2cellml-biomodels update [--models biomodels/models.json] [--count N]
sbml2cellml-biomodels report --results FILE --output FILE

run runs the pipeline over --ids or, by default, the selection file, writes the results and the report; it gives up without writing either when too many ids failed to download (DOWNLOAD_FAILURE_FRACTION, e.g. a BioModels outage) or when no case was left to run, and, when --results already exists, prints its regressions and improvements against the new run. update refreshes the selection file from the current BioModels search. report renders a results file. run and report write the bar diagram of the report next to it (images/biomodels.svg and images/biomodels_dark.svg).

The check is run locally, not in continuous integration: it downloads and simulates more than a thousand models.

build_parser ¶

build_parser()

Build the argument parser.

Returns:

Type	Description
`ArgumentParser`	The parser with the `run`, `update` and `report` subcommands.

main ¶

main(argv=None)

Run the command.

Parameters:

Name	Type	Description	Default
`argv`	`list[str] \| None`	arguments without the program name, `sys.argv[1:]` by default.	`None`

Returns:

Type	Description
`int`	0 on success, 1 on a missing selection or results file.