docs: fix master doc build (Attractors floor + latest SciML API adaption)#1490
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docs: fix master doc build (Attractors floor + latest SciML API adaption)#1490ChrisRackauckas-Claude wants to merge 2 commits into
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The Documentation workflow on master fails in the `dynamical_systems_basins`
`@example` block of `docs/src/steady_state_functionality/dynamical_systems.md`,
where `basins_of_attraction` errors with:
UndefVarError: `referenced_sciml_model` not defined in `Attractors`
@ Attractors .../src/mapping/attractor_mapping.jl:220
This is a version-skew between two DynamicalSystems-ecosystem packages.
DynamicalSystemsBase renamed `referrenced_sciml_model` -> `referenced_sciml_model`
(fixing the misspelling). Attractors 1.37.0 (the version the docs env resolved to)
calls `DynamicalSystemsBase.referenced_sciml_model` directly with no fallback, so
when paired with a DynamicalSystemsBase that only had the renamed/old symbol it threw.
Attractors 1.38.2 added an `isdefined(DynamicalSystemsBase, :referenced_sciml_model)`
guard that works with both the old (`referrenced_sciml_model`) and new
(`referenced_sciml_model`) names. Add `Attractors` as a direct docs dependency with
a `1.38.2` compat floor so the docs environment can no longer resolve to the broken
`Attractors < 1.38.2`. The page already uses `AttractorsViaRecurrences`,
`basins_of_attraction`, and `heatmap_basins_attractors` directly, so making
Attractors an explicit dependency is natural.
Verified locally on Julia 1.12: the failing `@example` block runs successfully with
Attractors 1.38.4 (resolved under the new floor), producing the two expected
fixed-point attractors with no UndefVarError.
Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
isaacsas
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Assuming docs build with this I approve.
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Is this the one that was solved here? |
The Documentation `build` job had many `@example` blocks failing after the latest SciML stack (OrdinaryDiffEq v2 / SciMLBase 3 / BifurcationKit 0.8 / SciMLLogging 2) introduced breaking API changes. Adapt the doc code: - `verbose = false` (Bool) is rejected by `solve` (DiffEqBase `_process_verbose_param`). Use `verbose = SciMLLogging.None()`; add `SciMLLogging` as a docs dependency and import it in the affected pages. - `Rodas5P(autodiff = false)` (Bool) is rejected; use `autodiff = AutoFiniteDiff()` (add `ADTypes` docs dep + import). - `EnsembleProblem` `prob_func` is now called as `prob_func(prob, ctx)` (where `ctx::EnsembleContext` exposes `ctx.sim_id`), not `prob_func(prob, i, repeat)`. - The OrdinaryDiffEq solver-level `precs` keyword moved to the LinearSolve linsolve: `Rodas5P(linsolve = KrylovJL_GMRES(precs = ...))` with the new 2-argument `precs(A, p) -> (Pl, Pr)` signature. - BifurcationKit renamed `PeriodicOrbitOCollProblem` to `Collocation`. - `LBFGSB` is now exported by both `Optim` and `OptimizationLBFGSB`, causing an ambiguity `UndefVarError`; qualify it as `OptimizationLBFGSB.LBFGSB()`. Each changed block was verified locally on Julia 1.12 (the Documentation workflow's version) by running it against the resolved docs environment. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
ChrisRackauckas-Claude
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This ais already handled in #1488, but I just need SciML/OrdinaryDiffEq.jl#3766 to be merged first. |
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Summary
The Documentation workflow on
master(jobbuild) was failing. The build runs all@exampleblocks and aggregates errors, and the full run surfaced 47 failing blocks across ~10 doc pages — all caused by breaking API changes in the latest SciML stack (OrdinaryDiffEq v2 / SciMLBase 3 / BifurcationKit 0.8 / SciMLLogging 2 / Attractors 1.38). This PR fixes them.Fixes
Attractors floor (original commit).
Attractors < 1.38.2callsDynamicalSystemsBase.referenced_sciml_modelwith no fallback; the rename broke thedynamical_systems_basinsblock. AddedAttractorsas a direct docs dep with a1.38.2compat floor.verbose = false(Bool) rejected bysolve. DiffEqBase's_process_verbose_param(::Bool)now throwsArgumentError. Replaced withverbose = SciMLLogging.None()(addedSciMLLoggingas a docs dep + per-page import). Affected:optimization_ode_param_fitting.md,behaviour_optimisation.md,global_sensitivity_analysis.md,turing_ode_param_fitting.md,ode_fitting_oscillation.md.Rodas5P(autodiff = false)(Bool) rejected. Replaced withautodiff = AutoFiniteDiff()(addedADTypesdocs dep + import) indynamical_systems.md.EnsembleProblemprob_funcsignature change. Nowprob_func(prob, ctx)withctx::EnsembleContext(index isctx.sim_id), notprob_func(prob, i, repeat). Updatedode_simulation_performance.md,ensemble_simulations.md,noise_modelling_approaches.md,turing_ode_param_fitting.md.Solver
precskeyword moved to LinearSolve.Rodas5P(linsolve = KrylovJL_GMRES(precs = ...))with the new 2-argprecs(A, p) -> (Pl, Pr)signature, replacing the old 9-arg OrdinaryDiffEq form, inode_simulation_performance.md.BifurcationKit rename.
PeriodicOrbitOCollProblem→Collocationinbifurcationkit_periodic_orbits.md.LBFGSBexport ambiguity. BothOptimandOptimizationLBFGSBnow exportLBFGSB, givingUndefVarErrorambiguity. Qualified asOptimizationLBFGSB.LBFGSB()inlikelihood_profiler.md.No tolerances were loosened and no blocks were skipped/disabled — every fix migrates the example to the current API.
Verification
On Julia 1.12 (the Documentation workflow's version), against the resolved docs environment, I ran each changed
@examplechain's load-bearing blocks end-to-end and confirmed they execute without error:verbose = SciMLLogging.None()optimization loss loop (loss = 0.0 at the true parameters).prob_func(prob, ctx)+EnsembleProblemsolve (5 trajectories, allSuccess).Rodas5P(autodiff = AutoFiniteDiff())→lyapunovspectrum(largest exponent positive → chaotic, as the page states).incompletelu(A, p)+KrylovJL_GMRES(precs = ...)+concrete_jac = truesolve completes (sparse problem).bifurcationdiagram→Collocation(50, 4)→continuation(...)returns a validBranch.OptimizationLBFGSB.LBFGSB()resolves cleanly with bothOptimandOptimizationLBFGSBloaded.Please ignore until reviewed by @ChrisRackauckas.