ReBop runtime-expression compatibility notice

Upstream compatibility target: Armavica/rebop 0.9.7 Upstream license: MIT Upstream copyright: 2021 Virgile Andreani

ReBop 0.9.7 defines a public Rate::expr(Expr) constructor and a public Rate::Expr(Expr) variant, but its crate root declares mod expr rather than pub mod expr. A dependent Rust crate therefore cannot name or construct the argument type. The Python binding can use it because it is inside the ReBop crate.

vendor/rebop/ is a reduced, tutorial-owned implementation derived from the relevant upstream behavior. It is not a one-line visibility patch or a source-identical copy. It carries only:

• the runtime expression tree and evaluator;
• sparse law-of-mass-action propensities;
• seeded Gillespie direct-method stepping; and
• the species, reaction-count, time and advance methods used by this tutorial.

Compared with upstream 0.9.7, it omits the dense rate/jump APIs, unseeded constructor, reseeding and state/time setters, macro DSL, Python binding, parser, benchmarks and unrelated documentation. Dense jumps are always converted to sparse storage, so the constructor’s sparse compatibility argument is accepted but has no effect. The local stepper also stops a path when an individual propensity is non-finite or negative; upstream only stops when the accumulated total is not positive.

The integration test in tests/upstream_compatibility.rs links both sources under distinct crate names. At seeds 1, 42 and 12345, it requires exact species counts and model times for the same sparse mass-action birth/conversion/decay network at several checkpoints. This gates the shared path used for degradation reactions. Upstream’s private Expr type prevents an external side-by-side test of runtime expressions; that path is instead a small semantic re-derivation covered by analytic propensity and seeded replay tests.

The main dependency selects the local rebop = "=0.9.7" path explicitly; the registry release is a dev-dependency used only by the compatibility test. The lockfile and run.json cache boundary identify the compatibility revision as rebop=0.9.7-expr-public-v1.

Replace the local dependency and this notice when a released ReBop version makes the runtime expression type constructible from external Rust without changing the model equations.