API reference¶
The API reference is generated from the docstrings of the package.
| module | description |
|---|---|
| sbml2cellml | Conversion of SBML models to CellML, convert_sbml2cellml |
| cellml2sbml | Conversion of CellML models to SBML, convert_cellml2sbml |
| cellml | Reading, writing and validating CellML models with libcellml |
| sbml | Reading, writing and validating SBML documents with libsbml |
| mathml | MathML fragments of the equations |
| astnodes | Construction of formulas as libsbml ASTs |
| metadata | Names, notes and annotations of the SBML elements as RDF next to the CellML model |
| sbmlmath | CellML maths (analyser AST, MathML) to libsbml ASTs |
| units | CellML units to SBML unit definitions |
| cellmlunits | SBML units to CellML units, the units of the variables |
| variables | SBML ids of the CellML variables |
| simulate | Timecourse simulation with libopencor (optional dependency) |
| cli | The sbml2cellml and cellml2sbml commands |
| console | Shared rich console |
| log | Logging of the package |
sbml2cellml.testsuite¶
The sbml2cellml-testsuite command runs the SBML test suite through both converters and both simulators, see SBML test suite and Development.
| module | description |
|---|---|
| testsuite.cases | Downloading the suite, reading and filtering the semantic test cases |
| testsuite.compare | Comparison of a simulation with the expected results of a case |
| testsuite.simulators | The roadrunner and libopencor simulator functions run inside a worker |
| testsuite.worker | Simulators in their own processes |
| testsuite.runner | The pipeline of the harness, five stages per case |
| testsuite.results | Results of a suite run: per case and stage, JSON, regressions |
| testsuite.report | Markdown report of a suite run, the page docs/testsuite.md |
| testsuite.figure | Bar diagram of a suite run, the figures docs/images/testsuite*.svg |
| testsuite.cli | The sbml2cellml-testsuite command |
sbml2cellml.biomodels¶
The sbml2cellml-biomodels command runs the manually curated SBML models of BioModels through the pipeline of the test suite, see BioModels and Development.
| module | description |
|---|---|
| biomodels.models | Access to the BioModels database: search, model info, download, selection |
| biomodels.cases | Case construction for a BioModels model |
| biomodels.runner | Runner producing the results from a BioModels selection |
| biomodels.cli | The sbml2cellml-biomodels command |