0.3.0

Release notes for sbmlode 0.3.0

sbmlode 0.3.0 writes the ODE system of an SBML model as python code of JAX, which diffrax simulates: jax.jit compiles the simulation, jax.vmap batches it over constants and initial states, and jax.grad and jax.jacfwd differentiate it, a model with events included. It passes every case of the SBML test suite which it supports and libroadrunner simulates. sbmlode requires python 3.12 or newer, as jax does.

New features

• the format diffrax (#8), written with system.write("model.py", fmt="diffrax") (.py stays the suffix of python): initial_values(p), f_dxdt(t, x, p) (a vector field of diffrax), f_y(t, x, p), the functions of the events, and with simulator=True simulate(ts, p, x0, ...), which returns a Simulation of the output times, states, assigned values and constants, and to_frame, its pandas DataFrame; the file switches JAX to float64 on import
• the events of SBML in JAX: delays, priorities, persistence, the initial values of the triggers, the values from the trigger time and cascades, on arrays of fixed shapes (max_segments, max_pending), in loops of the kind the adjoint of diffrax differentiates (RecursiveCheckpointAdjoint for jax.grad, ForwardMode for jax.jacfwd, DirectAdjoint for both); the derivative includes the shift of an event time with the constants
• default_solver(), diffrax.Kvaerno5 with Chord, a chord method which ends at an increment below kappa (patrick-kidger/diffrax#782); the steps of a model without events end at the output times
• JaxPrinter, the dialect jax of the math, which JAX traces: jnp.where for piecewise, the logic of jnp, float literals and jnp.power
• the extra diffrax (jax, diffrax, equinox, optimistix, pandas), which the generated code runs with
• scripts/ode_report.py --format diffrax, the pass rate of the diffrax code over the SBML test suite: all 1481 cases which are supported and which libroadrunner simulates

Documentation

• a section of the guide on the diffrax code, with jax.jit, jax.vmap, jax.grad and jax.jacfwd and a solve of one's own, the conventions of the formats in a compact table, the diffrax code of the repressilator and its row in the verification table
• the design of the diffrax export, docs/design/2026-10-06-diffrax-export-design.md

Breaking changes

• python 3.11 is no longer supported, sbmlode requires python 3.12 or newer

Your sbmlode team