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

0.2.0

Release notes for sbmlode 0.2.0

sbmlode 0.2.0 writes the ODE system in the native quantities of the SBML state variables: a species is a state in amount or in concentration as the model declares it, also in a compartment whose size changes. This changes the system and its typed target, see the breaking changes.

New features

• a species in concentration in a compartment whose size changes stays in concentration: its ODE is the one of SBML Level 3 Version 2, section 3.4.6, the reaction terms divided by the size minus the dilution S/V dV/dt (Ode.size_rate); a boundary, constant or not reacting species in such a compartment keeps its amount and is diluted alone (origin dilution) (matthiaskoenig/sbml4humans#114)
• the rate of the size of a compartment dV/dt is an assignment of its own (origin size_rate, OdeSystem.size_rates, a symbol of kind rate whose source is the compartment, typeset as the derivative of the compartment): the right hand side of its rate rule, or the derivative of its assignment rule by the chain rule; a size with an assignment rule of constants only is constant, a rule which cannot be differentiated is the unsupported construct rate of an assigned size
• astutil.derivative(ast, variable), the symbolic derivative of a math, simplified
• an event which changes a size rescales every species in concentration of the compartment with the size after the event, also when it changes a parameter of the assignment rule of the size; the code writes the function event_sizes_<id> of these sizes
• rateOf of a species in concentration in a variable compartment and of a size with an assignment rule

Documentation

• the logo of sbmlode in the README, the documentation, the release notes and as favicon

Breaking changes

• OdeSystem.amounts, Quantity.amount_of, Ode.amount_of, the origin concentration and the section amounts of the typed target and of the documents are removed, a species is never replaced by its amount n_S
• TypesetEventAssignment has no field species, its conversion is None or resized
• the code context of an event assignment has divisor_index into the new list sizes of the event instead of divisor_position

Your sbmlode team

0.1.0

Release notes for sbmlode 0.1.0

We are pleased to release the first version of sbmlode, the ODE export of sbmlutils as a package of its own. sbmlode writes the system of ordinary differential equations of an SBML model as python, julia and R code which simulates it and as typst, LaTeX and markdown documents which describe it. It depends on python-libsbml and jinja2 only, so that a tool which only needs the equations of a model, such as SBML4Humans, does not install the model building of sbmlutils.

New features

• the ODE export of sbmlutils 0.14.0 (sbmlutils.converters.ode, matthiaskoenig/sbmlutils#492) as the package sbmlode: OdeSystem.from_sbml(source), render(fmt, **options), write(path) and render_template(template) in the formats python, julia, R, typst, LaTeX and markdown, with the same output apart from the line which names the version that wrote it
• OdeSystem.typeset(dialect, symbols, wrap) returns the typeset system as typed data instead of a document: the ODEs, the reaction rates, the assignment rules, the function definitions, the initial values and the events with their left hand sides and right hand sides in LaTeX or typst, which an application lays out itself; the documents of typst, LaTeX and markdown are rendered from it
• wrap(symbol, typeset) is called for every symbol the typeset math writes, including the rate v of a reaction and the amount n of a species, so that an application can turn a symbol into a link to its element; Symbol.element names the element of the model a symbol stands for, the reaction and the id of a local parameter which the analysis renames

Packaging and development

• the package reads and flattens a document with libsbml alone (sbmlode.io) and writes the units of a model without pint (sbmlode.units)
• the tests download the semantic cases of the SBML test suite 3.4.0 once into the cache directory, or read the directory SBMLODE_TESTSUITE names; SBMLODE_JULIA and SBMLODE_RSCRIPT set the commands of julia and R
• continuous integration runs the suite on Linux, Windows and macOS, the generated R code with deSolve and the documents with tectonic and typst for every pull request, and the julia code for a release and on demand; the documentation is published at https://matthiaskoenig.github.io/sbmlode

Your sbmlode team