cli¶

The commands of a model.

A model package registers its commands in [project.scripts] with its model object, e.g. for hctz:

run_hctz = "pkdb_models.models.hctz:MODEL.run_main"
fit_hctz = "pkdb_models.models.hctz:MODEL.fit_main"
report_hctz = "pkdb_models.models.hctz:MODEL.report_main"
identifiability_hctz = "pkdb_models.models.hctz:MODEL.identifiability_main"

run_<model> creates the models with the factory and runs the simulation experiments:

run_hctz --action factory
run_hctz --action list_experiments
run_hctz --action simulate --experiments "misc,Anderson1961" --open
run_hctz --action all --results-dir /path/to/results

A single group is written into the directory of the group, any other selection into custom_selection, both in the simulation folder of the results. The output ends with the links to the report and to the figures.

fit_<model> fits the parameters of a fit problem and, with --identifiability (the default of a model with fit_identifiability), analyses the identifiability of the fitted parameters: the profile likelihood of every fitted parameter and the Fisher information around the best parameter set, which end up in the identifiability section of the report of the fit. report_<model> and identifiability_<model> work on the parameters.json of an earlier fit (sbmlsim.fit.cli.report_cli, identifiability_cli). All write into the results of the model unless --output_dir is given.

Action ¶

Bases: StrEnum

The actions of the run command, pkpdsim.model.RUN_ACTIONS.

parse_formats ¶

parse_formats(text)

Get the figure formats of a comma separated list.

Parameters:

Name	Type	Description	Default
`text`	`str`	the formats, e.g. `"svg, PNG"`.	required

Returns:

Type	Description
`list[str]`	The formats in lower case, without blanks and empty entries.

parse_workers ¶

parse_workers(text, model)

Get the processes of a run from the option --workers.

Parameters:

Name	Type	Description	Default
`text`	`str`	`model` for the setting of the model, `auto` for the choice of sbmlsim (`None`: a pool of every CPU for a scan of 256 points or more), or a positive number.	required
`model`	`PKPDModel`	the model.	required

Returns:

Type	Description
`int \| None`	The number of processes, `None` for the choice of sbmlsim.

Raises:

Type	Description
`ValueError`	for any other text.

resolve_experiments ¶

resolve_experiments(registry, names)

Resolve the names of groups and experiments to the experiment classes.

Parameters:

Name	Type	Description	Default
`registry`	`Mapping[str, Sequence[type[SimulationExperiment]]]`	the groups of experiments of a model.	required
`names`	`Sequence[str]`	names of groups or of experiment classes.	required

Returns:

Type	Description
`list[type[SimulationExperiment]]`	The experiment classes, every class once in the order of the names, and
`list[str]`	the names which are neither a group nor an experiment.

run_parser ¶

run_parser(model)

Get the parser of the run command of a model.

run_command ¶

run_command(model, args=None)

Run the action of the command line of run_<model>.

Parameters:

Name	Type	Description	Default
`model`	`PKPDModel`	the model.	required
`args`	`Sequence[str] \| None`	the command line arguments, `sys.argv[1:]` by default.	`None`

A failure of the simulations does not stop the command: the remaining actions run, then the failures are printed and the command exits with 1. An extra action gets the settings of the simulator of the run as options.simulator: those of the model with the processes of --workers.

with_output_dir ¶

with_output_dir(args, output_dir)

Add the output directory of the model to command line arguments.

The commands of sbmlsim.fit.cli write into the working directory by default, a model writes into its results instead.

Parameters:

Name	Type	Description	Default
`args`	`Sequence[str]`	command line arguments without the program name.	required
`output_dir`	`Path`	output directory used if the arguments do not name one.	required

Returns:

Type	Description
`list[str]`	The arguments with the output directory in front of them. argparse keeps
`list[str]`	the last value of an option, so an output directory in the arguments,
`list[str]`	also an abbreviation like `--out`, wins.

fit_parser ¶

fit_parser(model, definitions)

Get the parser of the fit command of a model.

The fit arguments are those of sbmlsim.fit.cli.fit_cli, the identifiability arguments are the settings of the profile likelihood which follows the fit.

analyse_identifiability ¶

analyse_identifiability(run, options)

Analyse the identifiability of the parameters of a finished fit.

The profile likelihood is the exact answer and the Fisher information the cheap local one next to it; both are computed around the best parameter set of the fit and end up in the identifiability section of its report.

Parameters:

Name	Type	Description	Default
`run`	`FitRun`	finished fit whose best parameter set is analysed.	required
`options`	`Namespace`	command line arguments of `fit_parser`.	required

Returns:

Type	Description
`tuple[IdentifiabilityResult \| None, FisherInformation \| None]`	The profiles and the Fisher information, `None` for what was skipped.

fit_command ¶

fit_command(model, args=None)

Run a fit of a model and analyse the identifiability of its parameters.

Parameters:

Name	Type	Description	Default
`model`	`PKPDModel`	the model.	required
`args`	`Sequence[str] \| None`	command line arguments, `sys.argv[1:]` by default.	`None`

Returns:

Type	Description
`dict[str, FitRun]`	The finished fits by optimization id.

report_command ¶

report_command(model, args=None)

Report stored parameter sets of a model (sbmlsim.fit.cli.report_cli).

Parameters:

Name	Type	Description	Default
`model`	`PKPDModel`	the model.	required
`args`	`Sequence[str] \| None`	command line arguments, `sys.argv[1:]` by default.	`None`

Returns:

Type	Description
`Path`	The directory of the report.

identifiability_command ¶

identifiability_command(model, args=None)

Analyse the identifiability of stored parameters of a model.

See sbmlsim.fit.cli.identifiability_cli.

Parameters:

Name	Type	Description	Default
`model`	`PKPDModel`	the model.	required
`args`	`Sequence[str] \| None`	command line arguments, `sys.argv[1:]` by default.	`None`

Returns:

Type	Description
`Path`	The directory of the report.