Emit Python observables from the model's assignment rules - #35
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A consumer scoring the model against data has to recompute the derived quantities the data names: totals, lineages, volume fractions. Those are repeatedAssignment rules the C++ emitter already reads, so emitting Python from the same SBML keeps the two in step. Re-deriving them by hand is a second definition that drifts, and on the PDAC model a hand expansion of the aggregate module had already missed phi_collagen, which lives in a different module and is a nonlinear ratio. resolve() closes a requested symbol set over the rules and returns the raw species it needs, which is the output contract for anything standing in for the simulator. It raises on unknown symbols and on cycles rather than dropping them. emit() writes pure arithmetic, so the module needs no array library and runs on floats, numpy arrays or JAX tracers alike. Non-arithmetic operators are refused where the rule is first read, so the error names the rule instead of reporting 'std' and 'max' as missing symbols. On PDAC: 35 symbols close to 30 states, 13 constants and 20 rules, and every aggregate identity reproduces exactly on random states.
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A consumer scoring the model against data has to recompute the derived quantities the data names: totals, lineages, volume fractions. Those are
repeatedAssignmentrules the C++ emitter already reads, so emitting Python from the same SBML keeps the two in step. Re-deriving them by hand is a second definition that drifts, and on the PDAC model a hand expansion of the aggregate module had already missedphi_collagen, which lives in a different module and is a nonlinear ratio.resolve()closes a requested symbol set over the rules and returns the raw species it needs, which is the output contract for anything standing in for the simulator. Raises on unknown symbols and on cycles rather than dropping them.emit()writes pure arithmetic, so the generated module needs no array library and runs on floats, numpy arrays or JAX tracers alike. Non-arithmetic operators are refused where the rule is first read, so the error names the rule instead of reportingstdandmaxas missing symbols.emit-observablessubcommand alongsidegenerateandverify.On PDAC: 35 symbols close to 30 states, 13 constants and 20 rules, and every aggregate identity reproduces exactly on random states.