Time unit conversion

[kwabenantim]

Fixes #15

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (73e0cdd) to head (dd3eb1a).

Additional details and impacted files

Flag	Coverage Δ
cpp	100.00% <100.00%> (ø)
python	100.00% <100.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
...s/src/reference/Chen2000/Chen2000SbmlOdeSystem.cpp	100.00% <100.00%> (ø)
...s/src/reference/Chen2000/Chen2000SbmlOdeSystem.hpp	100.00% <ø> (ø)
...s/src/reference/Chen2004/Chen2004SbmlOdeSystem.cpp	100.00% <100.00%> (ø)
...s/src/reference/Chen2004/Chen2004SbmlOdeSystem.hpp	100.00% <ø> (ø)
...reference/Gardner1998/Gardner1998SbmlOdeSystem.cpp	100.00% <100.00%> (ø)
...reference/Gardner1998/Gardner1998SbmlOdeSystem.hpp	100.00% <ø> (ø)
...rence/Goldbeter1991/Goldbeter1991SbmlOdeSystem.cpp	100.00% <100.00%> (ø)
...rence/Goldbeter1991/Goldbeter1991SbmlOdeSystem.hpp	100.00% <ø> (ø)
...els/src/reference/Tan2014/Tan2014SbmlOdeSystem.cpp	100.00% <100.00%> (ø)
...els/src/reference/Tan2014/Tan2014SbmlOdeSystem.hpp	100.00% <ø> (ø)
... and 13 more

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Copilot]

Pull request overview

This PR addresses SBML→Chaste time unit handling by introducing explicit time-unit detection/resolution and generating ODE systems that consistently scale time inputs and derivatives to Chaste’s default time base (hours), with a CLI override for ambiguous cases.

Changes:

• Add TimeUnit (ms/s/min/h/none), detect declared SBML time units, and resolve a final scaling choice (with warnings + --timescale override).
• Update ODE templates and checked-in reference models/tests to apply the chosen time scaling (including updated expectations/timesteps in CxxTests).
• Harden template rendering correctness (StrictUndefined + reject rendering None) and add a static template-context contract test.

Reviewed changes

Copilot reviewed 43 out of 43 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
chaste_sbml/tests/test_timescale.py	New unit + end-to-end tests for time-unit detection/resolution and codegen scaling output.
chaste_sbml/tests/test_template_contract.py	New static lint ensuring templates only reference provided context variables; checks no C++ escaping.
chaste_sbml/tests/test_sbml_reader.py	Updates for new load_sbml_model return values; adds unsupported-level warning tests.
chaste_sbml/tests/test_model_builder.py	Updates to unpack new load_sbml_model tuple return.
chaste_sbml/templates/ode/ode.hpp	Removes unused “stoichiometry variables” section from the generated header.
chaste_sbml/templates/ode/ode.cpp	Adds conditional time scaling (multiplier const, scaling in derivatives/derived quantities/events).
chaste_sbml/SbmlRefModels/test/reference/TestTysonNovak2001SbmlOdeSystem.hpp	Adjusts solver times/derivative comparisons for minute→hour scaling.
chaste_sbml/SbmlRefModels/test/reference/TestTysonNovak2001SbmlCellCycleModel.hpp	Adjusts SimulationTime dt/end-time and comparisons for minute→hour scaling.
chaste_sbml/SbmlRefModels/test/reference/TestTan2014SbmlSrnModel.hpp	Adjusts SimulationTime spans for minute→hour scaling.
chaste_sbml/SbmlRefModels/test/reference/TestTan2014SbmlOdeSystem.hpp	Adjusts dt/end-time and derivative comparisons for minute→hour scaling.
chaste_sbml/SbmlRefModels/test/reference/TestGoldbeter1991SbmlSrnModel.hpp	Adjusts SimulationTime spans for second→hour scaling.
chaste_sbml/SbmlRefModels/test/reference/TestGoldbeter1991SbmlOdeSystem.hpp	Adjusts dt/end-time and derivative comparisons for second→hour scaling.
chaste_sbml/SbmlRefModels/test/reference/TestGardner1998SbmlOdeSystem.hpp	Adjusts dt/end-time and derivative comparisons for second→hour scaling.
chaste_sbml/SbmlRefModels/test/reference/TestGardner1998SbmlCellCycleModel.hpp	Adjusts SimulationTime dt/end-time for second→hour scaling.
chaste_sbml/SbmlRefModels/test/reference/TestChen2004SbmlOdeSystem.hpp	Adjusts stop-time + derivative comparisons for minute→hour scaling.
chaste_sbml/SbmlRefModels/test/reference/TestChen2004SbmlCellCycleModel.hpp	Adjusts SimulationTime dt/end-time and comparisons for minute→hour scaling.
chaste_sbml/SbmlRefModels/test/reference/TestChen2000SbmlOdeSystem.hpp	Adjusts dt/end-time and derivative comparisons for minute→hour scaling.
chaste_sbml/SbmlRefModels/test/reference/TestChen2000SbmlCellCycleModel.hpp	Adjusts SimulationTime dt/end-time for minute→hour scaling.
chaste_sbml/SbmlRefModels/src/reference/VanLeeuwen2007NonDim/VanLeeuwen2007NonDimSbmlOdeSystem.hpp	Removes unused “stoichiometry variables” comment block in checked-in generated header.
chaste_sbml/SbmlRefModels/src/reference/VanLeeuwen2007NonDim/VanLeeuwen2007NonDimSbmlOdeSystem.cpp	Removes obsolete “TODO: Scale time appropriately” comment in checked-in generated source.
chaste_sbml/SbmlRefModels/src/reference/VanLeeuwen2007/VanLeeuwen2007SbmlOdeSystem.hpp	Removes unused “stoichiometry variables” comment block in checked-in generated header.
chaste_sbml/SbmlRefModels/src/reference/VanLeeuwen2007/VanLeeuwen2007SbmlOdeSystem.cpp	Removes obsolete “TODO: Scale time appropriately” comment in checked-in generated source.
chaste_sbml/SbmlRefModels/src/reference/VanLeeuwen2007/VanLeeuwen2007.xml	Adds explicit unitDefinition id="time" to declare hours (via seconds×3600) for detection.
chaste_sbml/SbmlRefModels/src/reference/TysonNovak2001/TysonNovak2001SbmlOdeSystem.hpp	Removes unused “stoichiometry variables” comment block in checked-in generated header.
chaste_sbml/SbmlRefModels/src/reference/TysonNovak2001/TysonNovak2001SbmlOdeSystem.cpp	Adds minute→hour time/derivative scaling logic in checked-in generated source.
chaste_sbml/SbmlRefModels/src/reference/Tan2014/Tan2014SbmlOdeSystem.hpp	Removes unused “stoichiometry variables” comment block in checked-in generated header.
chaste_sbml/SbmlRefModels/src/reference/Tan2014/Tan2014SbmlOdeSystem.cpp	Adds minute→hour time/derivative scaling logic in checked-in generated source.
chaste_sbml/SbmlRefModels/src/reference/Goldbeter1991/Goldbeter1991SbmlOdeSystem.hpp	Removes unused “stoichiometry variables” comment block in checked-in generated header.
chaste_sbml/SbmlRefModels/src/reference/Goldbeter1991/Goldbeter1991SbmlOdeSystem.cpp	Adds second→hour time/derivative scaling logic in checked-in generated source.
chaste_sbml/SbmlRefModels/src/reference/Gardner1998/Gardner1998SbmlOdeSystem.hpp	Removes unused “stoichiometry variables” comment block in checked-in generated header.
chaste_sbml/SbmlRefModels/src/reference/Gardner1998/Gardner1998SbmlOdeSystem.cpp	Adds second→hour time/derivative scaling logic in checked-in generated source.
chaste_sbml/SbmlRefModels/src/reference/Chen2004/Chen2004SbmlOdeSystem.hpp	Removes unused “stoichiometry variables” comment block in checked-in generated header.
chaste_sbml/SbmlRefModels/src/reference/Chen2004/Chen2004SbmlOdeSystem.cpp	Adds minute→hour time/derivative scaling logic in checked-in generated source.
chaste_sbml/SbmlRefModels/src/reference/Chen2000/Chen2000SbmlOdeSystem.hpp	Removes unused “stoichiometry variables” comment block in checked-in generated header.
chaste_sbml/SbmlRefModels/src/reference/Chen2000/Chen2000SbmlOdeSystem.cpp	Adds minute→hour time/derivative scaling logic in checked-in generated source.
chaste_sbml/SbmlRefModels/generate_cases.py	Forces semantic cases to be time-dimensionless (TimeUnit.NONE) and simplifies case generation path.
chaste_sbml/chaste_sbml_model.py	Adds time_unit override, resolves time scaling policy, and injects new template vars.
chaste_sbml/_sbml_reader.py	Extends loader to return (model, declared unit, SBML level); adds time-unit detection helpers and level warnings.
chaste_sbml/_rendering.py	Disables autoescape explicitly; enforces StrictUndefined + fails fast when rendering None.
chaste_sbml/_records.py	Adds Equation.label field to keep template parity (avoid missing label lookups).
chaste_sbml/_model_builder.py	Removes unused time-scaling stub and no-longer-used template vars from builder output.
chaste_sbml/_config.py	Introduces TimeUnit enum with seconds factor matching and C++ literal rendering.
chaste_sbml/main.py	Adds --timescale CLI option and wires it into ChasteSbmlModel.

Suppressed comments (1)

chaste_sbml/templates/ode/ode.cpp:129

• When time scaling is enabled (scale_time), Initialise(double time) still receives Chaste time in hours but does not convert it to the model’s native units before evaluating the initial equation assignments. If any initial assignments / rules reference time (or if Initialise is ever called with nonzero time), those values will be computed in the wrong units, making the ODE system inconsistent with EvaluateYDerivatives/ProcessModelEvents which do scale time.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 43 out of 43 changed files in this pull request and generated no new comments.

Suppressed comments (1)

chaste_sbml/_config.py:111

• TimeUnit.from_cli currently raises a bare KeyError for unknown tokens. Since this method can be called outside the argparse-protected CLI, a ValueError with a clearer message would be a more appropriate public API failure mode.