Command-line options¶

The chaste-sbml command has two modes:

Generate (the default): convert an SBML file to Chaste C++ code.
Copy base classes (--copy-base-classes): copy out the C++ base classes the generated code depends on, instead of generating.

usage: chaste-sbml [-h] [--version] [--copy-base-classes]
                   [--output-dir OUTPUT_DIR]
                   [--model-type [{generic,srn,cell-cycle}]]
                   [--tests | --no-tests] [--timescale {ms,s,m,h}]
                   [--test-output-dir TEST_OUTPUT_DIR]
                   [sbml_file]

Positional argument¶

sbml_file: The SBML file to convert. Required when generating; must not be given in copy mode.

General options¶

-h, --help: Show the help message and exit.
--version: Show the program’s version number and exit.
--output-dir OUTPUT_DIR: The directory to place output files in. Applies to both modes. Defaults to the current directory.

Generation options¶

These apply only when generating code. Passing any of them together with --copy-base-classes is a usage error.

--model-type [{generic,srn,cell-cycle}]

The type of Chaste class to generate (default: generic).

generic: An ODE system only.
srn: A subcellular reaction network model wrapping the ODE system.
cell-cycle: A cell-cycle model wrapping the ODE system.

See Anatomy of generated code for the files each type produces.

--tests, --no-tests

Generate placeholder test files (default: off). Pass --tests to opt in; --no-tests restates the default. The placeholder is a CxxTest skeleton — see the placeholder test.

--timescale {ms,s,m,h}

The model’s native time unit — milliseconds, seconds, minutes, or hours — used to scale derivatives into Chaste’s hours. Overrides auto-detection from the SBML; omit it to auto-detect. See Time units below.

--test-output-dir TEST_OUTPUT_DIR

The directory to place generated test files in. Defaults to --output-dir, so set this to keep tests separate from the model source. Passing it implies --tests, since asking where the test goes asks for one; an explicit --no-tests still wins.

Copying the base classes¶

The generated code subclasses base classes such as AbstractSbmlOdeSystem, AbstractSbmlSrnModel, and AbstractSbmlCellCycleModel. They ship with the package; copy them into your project so they match the installed version of the tool:

chaste-sbml --copy-base-classes --output-dir src/

Important

In copy mode only --output-dir applies. Passing an SBML file or any generation option (such as --model-type or --no-tests) is a usage error, so mistakes are reported rather than silently ignored.

Time units¶

Chaste works in hours, so the generator scales the model’s derivatives from the model’s native time unit into hours. The unit is resolved with this precedence:

An explicit --timescale override wins. If it contradicts a unit declared by the model, a warning is logged and the override is used.
Otherwise a unit declared by the model is used.
Otherwise the SBML default applies:
- Level 2 predefines the time unit as seconds.
- Level 3 leaves an unset time unit undefined, so no conversion is applied.

When no unit is declared and none is given, a warning hints at --timescale. Auto-detection only recognises a time unit that reduces to seconds (second, millisecond, minute, hour); a composite or otherwise non-second time unit is treated as undeterminable, and you should pass --timescale explicitly.