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Changelog

Source: NEWS.md

odelia 0.3.1

Removes util::to_string_g(), added in 0.3.0 an hour earlier as a duplicate of util::format_double(). Both formatted a double for an error message with six significant figures — "%g" and "%.6g" are the same format string, since %g’s default precision is 6 — and they were byte-identical on every value tried. The one call site, in the invariant-rejection failure message, now uses format_double; its output is unchanged.

The duplicate arose because #55 was developed on a branch stacked below the 0.2.2 work that introduced format_double. Worth recording as a hazard rather than a review miss: two helpers with different names in different parts of the same file merge with no textual conflict, so neither the rebase nor the diff had anything to show.

A patch bump, although the header core lost a public symbol — the situation that earned 0.2.0 a minor one. The difference is what a version number can usefully say. 0.2.0’s removals had been reachable across released versions, so the bump warned of a break a consumer could actually hit. to_string_g never left this repository: 0.3.0 was never tagged — v0.2.1 remains the only tag and the only release — and both consumers are still on odelia (>= 0.2.x) with @v0.2.1 remotes. Nothing can have compiled against it, so a minor bump would announce an incompatibility that has no possible victim, and spend the signal for nothing.

Downstream floors are deliberately not raised. Neither plant nor phylloptim uses ode_state_valid() yet, and per the precedent set for leaf in 0.2.1 — checked rather than aligned for symmetry — raising a floor forces an upgrade for a change the consumer does not use. They should move to odelia (>= 0.3.0) when plant#609 or plant#599 actually adopts the domain check; 0.3.0 is the version that introduced it, and this release does not change it.

The 0.3.0 entry below has been corrected accordingly; it advertised a function that no longer exists.

odelia 0.3.0

Invariant-aware step rejection (#55). A system may now declare the domain its state lives in, and the adaptive stepper will refuse to commit a step that leaves it. Two ways to say so, both opt-in:

  • an optional bool ode_state_valid(const state_type&) const on the system, checked after each completed step;
  • util::stop_domain(msg), which throws the new util::DomainError, from anywhere in a stage.

Either one turns the step into a rejection — shrink and retry — rather than a committed out-of-domain state or, in the throwing case, a dead solve. Previously a throw from a stage ended the whole integration even though the pre-step state was still on the stack one frame up.

Only DomainError is caught. util::stop() and everything else still propagate, which is the point: absorbing them would turn a programming error into step-shrinking until “Cannot achieve the desired accuracy”, a diagnostic that points at the solver instead of at the bug.

This matters for bounded quantities that a finite RK step can overshoot even when the exact flow cannot — a carbon pool at zero, soil water at saturation, a probability at one. It is a discretisation guard, not a way to fix a model whose exact flow leaves its domain: that case shrinks to the minimum step and raises, now naming the reason and the location rather than blaming accuracy.

Version bumped so downstreams can pin against the capability (odelia (>= 0.3.0)); systems declaring neither hook are unaffected, and a Lorenz trajectory over 4127 steps is bit-identical across the change.

Numbers in that message are rendered with util::format_double(), so a step size at its floor reads 1e-08 rather than the "0.000000" std::to_string would give.

odelia 0.2.2

An out-of-domain interpolator lookup now says which point, how far out, and what the domain was. Interpolator::eval() had all three in hand — u, min() and max() — and reported none of them:

Extrapolation disabled and evaluation point outside of interpolated domain.

That sentence is the same whichever spline threw it, so a consumer holding several of them learns nothing about which one, and nothing about whether the point missed the near end or the far end. It cost real time downstream: localising traitecoevo/plant#576 meant instrumenting four call sites by hand to discover which spline was being asked and at what value, and the answer — the lower end, not past the far end as everyone had assumed — inverted the fix. Now:

Extrapolation disabled and evaluation point outside of interpolated domain:
u = -0.0023 lies 0.0023 beyond the lower end of [0, 6.8918].

Which spline, and which caller, is the one thing this layer cannot know; consumers that build several should catch and add it. A patch bump so downstreams can pin against the message.

Behaviour is otherwise unchanged. In particular the guard is still written u < min() || u > max() rather than the negation of an in-range test, because every comparison against NaN is false and a non-finite u must keep falling through to the spline — plant relies on that.

odelia 0.2.1

A patch bump for one reason: #46 has no version number, and a downstream needs one. d8235d1 (“Let a system compute its rates when the solver reads them”, #46) landed after 3bdfcf7 bumped the version to 0.2.0, and the version has not moved since — so 0.2.0 names two different header sets, one with #46 and one without, and no >= requirement can tell them apart.

That is not academic. traitecoevo/plant’s develop does not compile against the released 0.2.0:

odelia/ode_interface.hpp:212:3: error: 'this' argument to member function 'ode_rates'
  has type 'const plant::Patch<plant::FF16_Strategy, plant::FF16_Environment>',
  but function is not marked const

plant #585 made Patch::ode_rates non-const; r_ode_rates(const T& obj) and ode_solver_internal.hpp:155 both call it on a const&. #46 is the fix. Eight errors, four templated <Strategy, Environment> pairs × two call sites, and they surface inside these headers, which points nowhere near the cause. Confirmed pre-existing by syntax-checking plant’s origin/develop unmodified.

This is the same job 0.2.0 was bumped for, and the 0.2.0 entry below says so in as many words: it exists “to give downstream packages something to pin against … so a build against an older odelia fails at dependency resolution with a clear message rather than at compile time”. #46 needed the same courtesy and did not get it.

No header changes. Only DESCRIPTION. Downstream floors after this:

  • plant -> odelia (>= 0.2.1), because it links the ODE solver and needs #46.
  • leaf stays at odelia (>= 0.2.0). Checked rather than aligned for symmetry: leaf includes exactly one odelia header, odelia/interpolator.hpp, and never touches ode_rates or the solver. Raising its floor would force an upgrade for a fix in a header it does not include.

Closes #48.

odelia 0.2.0

A minor-version bump rather than a patch, because the header core lost public symbols: util::index, util::index_vector() and the base_1_to_0 / base_0_to_1 helpers are gone, and util::stop / util::warning no longer call into Rcpp. Nothing in the family used them — plant has its own plant::util equivalents — but a consumer that did would fail to compile, which is exactly what a version number is for. It also gives downstream packages something to pin against: leaf now requires odelia (>= 0.2.0), so a build against an older odelia fails at dependency resolution with a clear message rather than at compile time with RcppCommon.h: No such file or directory.

  • The header-only solver core is now free of R (#43). ode_util.hpp no longer includes RcppCommon.h, so everything reachable through interpolator.hpp, ode_control.hpp and ode_solver.hpp compiles and runs as plain C++ with no R installation — see tests/standalone/, which integrates the Lorenz system on a runner that has no R on it. util::stop() now throws std::runtime_error instead of calling Rcpp::stop(); Rcpp converts that into an ordinary R error with the same message at the package boundary, so R-level behaviour is unchanged apart from the condition’s class vector, which gains std::runtime_error in place of Rcpp::exception. util::warning() writes to std::cerr rather than raising an R warning; it had no callers. The unused util::index struct, its undefined Rcpp::as/wrap specializations, util::index_vector() and the base_1_to_0/base_0_to_1 helpers are removed — plant has its own. R remains where it belongs, in src/ and in solver_interface.hpp / rcpp_interface_helpers.hpp.

odelia 0.1.0

Odelia is a new package, arising out of https://github.com/traitecoevo/plant/. In that project, Rich FitzJohn built a custom ODE solver, using a Runge-Kutta 4-5 method, in C++. I’m spinning that code out into a package, as I want to use it elsewhere.

  • New implicit, adaptive-step RODAS4(3) Rosenbrock stepper for stiff systems, selectable via method = "rodas" when constructing a solver (#35). It reuses the existing adaptive step-size controller and obtains an exact Jacobian by forward-mode automatic differentiation; systems opt in by providing a template<class U> System<U> rebind() method. The explicit RKCK 4(5) method (method = "rkck") remains the default.

  • odelia now loads its shared library with global symbol visibility in .onLoad, so packages that LinkingTo: odelia and instantiate Solver can resolve the compiled XAD runtime symbols at load time without per-package linker hacks (#26).