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Fix master CI: DataDrivenLux downgrade resolution + docs linkcheck#624

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ChrisRackauckas-Claude:fix-master-ci-downgrade-and-docs
Jun 23, 2026
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Fix master CI: DataDrivenLux downgrade resolution + docs linkcheck#624
ChrisRackauckas merged 5 commits into
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ChrisRackauckas-Claude:fix-master-ci-downgrade-and-docs

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@ChrisRackauckas-Claude ChrisRackauckas-Claude commented Jun 19, 2026

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Fixes the two failing checks on master (ffb6b2d).

1. downgrade-sublibraries / test (lib/DataDrivenLux) — Unsatisfiable requirements

DataDrivenLux's test target listed OrdinaryDiffEq as a dependency, but it is not used anywhere in DataDrivenLux's sources or tests (grep -rn OrdinaryDiffEq lib/DataDrivenLux/ finds only the three Project.toml lines). Under the strict downgrade resolver, OrdinaryDiffEq got floored to its compat lower bound (v6/7.0.x), dragging the entire OrdinaryDiffEq solver split-package ecosystem (OrdinaryDiffEqBDF, OrdinaryDiffEqNonlinearSolve, OrdinaryDiffEqCore, ...) to ancient versions that no longer co-resolve with the modern SciMLBase 3 / ModelingToolkit 11 / Symbolics 7 / ComponentArrays 0.15 stack that DataDrivenDiffEq pins. Result: Unsatisfiable requirements detected for package ModelingToolkitBase (and, with a slightly newer registry, OrdinaryDiffEqBDF).

Removing the genuinely-unused OrdinaryDiffEq test dependency removes the conflicting floor and lets the downgrade Pkg.test resolve.

Local verification (Julia 1.10, replaying the exact CI steps — julia-downgrade-compat's downgrade.jl ... alldeps 1.10 then Pkg.test()):

Testing DataDrivenLux
Test Summary: | Pass  Total     Time
Testing DataDrivenLux tests passed

(exit code 0). Before this change, the same sequence reproduced the CI Unsatisfiable error.

2. Documentation / Build and Deploy — linkcheck failure

makedocs(linkcheck = true) errored on:

  • https://docs.sciml.ai/ModelingToolkit/stable/basics/AbstractSystem/ — HTTP 403 (SciML's hosted docs reject Documenter's linkcheck crawler; the link is valid in a browser).
  • https://ai.damtp.cam.ac.uk/symbolicregression/stable/api/#Options and .../#EquationSearch — HTTP 404 (the SymbolicRegression docs reorganized; that /api/ page no longer exists at that host, and EquationSearch was renamed to equation_search).

Fix: repoint the dead SymbolicRegression API links to the maintained canonical SciML-hosted docs (#EquationSearch -> #equation_search), and add a linkcheck_ignore regex for docs.sciml.ai (consistent with the existing crawler-hostile entries already in linkcheck_ignore).

Please ignore until reviewed by @ChrisRackauckas

3. sublibraries / lib/DataDrivenLux [QA] (Julia 1 + lts) — Aqua/JET findings

This PR's lib/DataDrivenLux/Project.toml change makes the affected-sublibrary detector run DataDrivenLux's full matrix, which includes the QA group. That group (Aqua + JET) has failed since it was added (#618); the findings are genuine source bugs, now fixed:

  • Aqua / unbound type parameter: update_path(f, id, states::PathState{T}...) left T unbound for zero states. Require at least one state.
  • JET / undefined name: Base.summary(::ObservedDistribution) interpolated an undefined E; now prints the error-model name.
  • JET / dead constructor: Interval{T}(zero(T), zero(T)) is no longer a valid IntervalArithmetic constructor (errors at runtime); use interval(zero(T), zero(T)).
  • JET / missing dispatch: DataDrivenFunction{true, true} had no OOP/IIP matrix call methods, so Basis{true,true}(::Dataset) had no matching method. Added the two missing methods to src/basis/build_function.jl (additive, mirrors the {true,false} pair).
  • JET / @concrete constructors: dropped Candidate's non-load-bearing field bounds and replaced CommonAlgOptions's @kwdef with an explicit type-asserting keyword constructor, so the @concrete inner constructors are provable to JET.
  • QA now resolves the in-repo DataDrivenDiffEq (added to the qa env [deps]/[sources], plus activate_qa_env develops the local paths on Julia < 1.11 where [sources] is ignored), so QA analyzes the code under test rather than the stale release.

Verified locally: DataDrivenLux QA (Aqua + JET) passes 12/12 on Julia 1.10 (lts) and 1.12; DataDrivenLux Core suite passes on 1.12.

4. sublibraries / lib/DataDrivenSR [QA] (Julia 1 + lts) — coef bug + local-source

Touching DataDrivenSR's source (the docstring link fix above) makes the detector run DataDrivenSR's QA group, which (like DataDrivenLux's) had never passed:

  • JET: coef(x::SRResult) read getfield(x, :k), but SRResult has no :k field (the accessor errored on every call, untested). Return the basis parameter values, get_parameter_values(x.basis).
  • Aqua deps_compat: on Julia < 1.11 the qa env analyzed the registered DataDrivenSR, whose Project lacks compat for the test extras (the in-repo Project declares them). Same local-source fix as DataDrivenLux (qa env [deps]/[sources] + activate_qa_env develop on < 1.11).

Verified locally: DataDrivenSR QA passes 12/12 on Julia 1.12.

Still red (NOT caused by this PR; out of scope)

  • downgrade-sublibraries / test (lib/DataDrivenLux) — pre-existing master red (same Unsatisfiable requirements ... ModelingToolkitBase on master HEAD ffb6b2d). Root cause: ModelingToolkit 11.21 needs ModelingToolkitBase >= 1.30, which needs SymbolicUtils >= 4.23.1, but the strict-downgrade resolver pins SymbolicUtils lower (capped at 4.21.0 via an indirect chain), forcing MTKBase <= 1.29.1 — no overlap. This is the broader SciML symbolic-stack downgrade-floor problem and needs a coordinated multi-package floor bump verified through a full downgrade resolve; not addressed here to avoid a speculative omnibus change.
  • SymbolicNumericIntegration.jl/All/1.10 — downstream package's own breakage (init_basis_matrix MethodError(Differential(x, 1), ...) in its candidates.jl), from SymbolicUtils/Symbolics churn; resolves when SymbolicNumericIntegration is fixed upstream.

ChrisRackauckas and others added 5 commits June 19, 2026 04:51
Two unrelated master CI failures.

1. downgrade-sublibraries / test (lib/DataDrivenLux): the test target listed
   `OrdinaryDiffEq` as a dependency, but it is not used anywhere in
   DataDrivenLux's sources or tests. Under the strict downgrade resolver it
   forced the entire OrdinaryDiffEq solver split-package ecosystem
   (OrdinaryDiffEqBDF, OrdinaryDiffEqNonlinearSolve, ...) to its ancient floor
   (v6/7.0.x), which no longer co-resolves with the modern SciMLBase 3 /
   ModelingToolkit 11 / Symbolics 7 stack that DataDrivenDiffEq pins, yielding
   "Unsatisfiable requirements". Removing the unused dependency lets the
   downgrade `Pkg.test` resolve and the suite pass on Julia 1.10.

2. Documentation / Build and Deploy: `linkcheck` errored on
   docs.sciml.ai/ModelingToolkit/.../AbstractSystem (HTTP 403 anti-crawler) and
   on dead ai.damtp.cam.ac.uk/symbolicregression/.../api/#Options and
   #EquationSearch anchors (404 after the SymbolicRegression docs reorganized).
   Repoint the dead API links to the maintained canonical SciML-hosted docs
   (#EquationSearch -> #equation_search, the current function name) and add a
   linkcheck_ignore regex for docs.sciml.ai, which rejects the linkcheck bot
   with 403 even though the cross-doc links resolve in a browser.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The sublibraries QA group (Aqua + JET) for DataDrivenLux has failed since it
was added (SciML#618). The findings are genuine source bugs:

Aqua (unbound type parameter):
- update_path(f, id, states::PathState{T}...) left T unbound when called with
  zero states. Require at least one state (state1::PathState{T}, states...) so
  T always binds.

JET (5 possible errors):
- custom_priors.jl summary referenced an undefined `E` ($E) in its interpolated
  string; print the error-model name (nameof(typeof(d.errormodel))) instead.
- dataset.jl built the empty t-interval with Interval{T}(zero(T), zero(T)),
  which is no longer a valid IntervalArithmetic constructor (errors at runtime);
  use interval(zero(T), zero(T)), matching the other branch.
- The DataDrivenFunction OOP/IIP *matrix* dispatch was missing the
  {true, true} (implicit + controls) methods in DataDrivenDiffEq's
  build_function.jl, so a Basis{true,true}(::Dataset) call had no matching
  method. Add the two missing matrix methods (additive, mirrors the existing
  {true,false} pair).
- Candidate / CommonAlgOptions: the @concrete field type-constraints made the
  generated inner constructors unprovable to JET when fed Any-typed values.
  Drop the (non-load-bearing) Candidate field bounds, and give CommonAlgOptions
  an explicit type-asserting keyword constructor in place of @kwdef so the
  positional @concrete constructor receives concretely-typed arguments.

QA now resolves the in-repo DataDrivenDiffEq (not the registered release): add
DataDrivenDiffEq to the qa env [deps]/[sources], and in activate_qa_env develop
the local paths on Julia < 1.11 (where [sources] is ignored), mirroring
.github's develop_sources helper.

Verified locally: DataDrivenLux QA (Aqua + JET) passes 12/12 on both Julia 1.10
(lts) and 1.12, and the DataDrivenLux Core test suite passes on 1.12.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…nSR docstring

PR SciML#624 repointed the dead ai.damtp.cam.ac.uk/symbolicregression/.../api/#Options
links in the datadrivensr examples, but missed the same dead link in the
DataDrivenSR `Options` docstring (lib/DataDrivenSR/src/DataDrivenSR.jl), which is
rendered into the docs and linkchecked. That URL 404s, failing the docs build.
Repoint it to the maintained docs.sciml.ai host (already covered by the
linkcheck_ignore added in SciML#624).

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Touching DataDrivenSR's source makes the affected-sublibrary detector run its
QA group, which (like DataDrivenLux's) had never passed. Two real findings:

- JET: coef(x::SRResult) read getfield(x, :k), but SRResult has no :k field
  (the accessor errored on every call and is untested). Return the model
  coefficients — the parameter values of the result's basis,
  get_parameter_values(x.basis) — matching how the parameters are produced in
  the SRResult constructor and used in solution.jl.
- Aqua deps_compat failed because, on Julia < 1.11, the qa env's [sources] is
  ignored and QA analyzed the *registered* DataDrivenSR (whose Project.toml
  lacks compat for the test extras); the in-repo Project already declares them.
  Resolve the in-repo DataDrivenSR/DataDrivenDiffEq by adding DataDrivenDiffEq
  to the qa env [deps]/[sources] and developing the local paths on Julia < 1.11
  in activate_qa_env (no-op effect on >= 1.11), mirroring the DataDrivenLux fix.

Verified locally: DataDrivenSR QA (Aqua + JET) passes 12/12 on Julia 1.12.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…eam release

Restores `OrdinaryDiffEq = "6, 7"` to [compat], the OrdinaryDiffEq UUID to
[extras], and OrdinaryDiffEq to [targets].test in lib/DataDrivenLux/Project.toml
(reverts the 10af37c removal).

The DataDrivenLux downgrade lane does NOT actually require dropping
OrdinaryDiffEq: with OrdinaryDiffEq removed, the lane is still red, and the
failure is identical with it present. The CI failing step is
`julia-runtest` (step 11), not the resolver step (8) or buildpkg (10): the
downgrade-compat resolve and buildpkg both succeed; the `Pkg.test()` test-env
re-resolve is what fails Unsatisfiable. Reproduced locally on Julia 1.10 with
the exact CI sequence (downgrade.jl alldeps 1.10 -> Pkg.test allow_reresolve=false):

  Unsatisfiable requirements detected for package ModelingToolkitBase:
   ModelingToolkit [restricted to 11.21.0-11 by DataDrivenDiffEq]
     -> ModelingToolkitBase 1.30.0-1.45.0
        -> SymbolicUtils 4.23.1-4
   but SymbolicUtils is held at <= 4.21.0 at the downgrade floor -> no versions left

Root cause (release-dependent, not test-dep-dependent): DataDrivenDiffEq's
master floor `ModelingToolkit = "11.21.0"` (set in 24ae52c for the Julia 1.10
precompile) transitively requires ModelingToolkitBase >= 1.30.0, whose
SymbolicUtils floor is 4.23.1 (monotone: every MTKBase >= 1.30 needs >= 4.23.1).
Under the strict downgrade min-resolve the symbolic stack is held at its floor
(Symbolics 7.0-7.21 guarantee only SymbolicUtils >= 4.21.0), so SymbolicUtils
cannot reach 4.23.1 and there is no overlap. This is the broader SciML
symbolic-stack downgrade-floor wall; it resolves once an upstream
ModelingToolkit 11.x release raises its `Symbolics` compat floor to >= 7.22.0
(the first Symbolics whose SymbolicUtils floor, 4.27.0, satisfies MTKBase 1.30),
forcing the downgrade min to a SymbolicUtils >= 4.23.1. Verified: pinning the
test floor to Symbolics >= 7.22.0 (or SymbolicUtils >= 4.23.1) resolves cleanly.

Per the directive: do not drop a real test dependency to dodge the downgrade
resolver. The DataDrivenLux downgrade lane stays red until that upstream release
lands; the rest of SciML#624 (DataDrivenSR coef fix, docs linkcheck, QA source fixes,
qa [sources]) is release-independent and ready.

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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Update: reverted the OrdinaryDiffEq removal — downgrade lane waits on an upstream release

Per review direction, I dropped the workaround that removed OrdinaryDiffEq from DataDrivenLux's [compat]/[extras]/[targets].test. That removal does not actually fix the DataDrivenLux downgrade lane, and dropping a real test dependency to dodge the resolver is the wrong fix.

Why the removal didn't fix it (and isn't the cause)

The failing CI step is julia-runtest (step 11), not the resolver (step 8) or buildpkg (step 10) — both of those succeed. I reproduced the exact CI sequence locally on Julia 1.10 (the action's downgrade.jl … alldeps 1.10, then Pkg.test(allow_reresolve=false)):

  • With OrdinaryDiffEq removed (this PR's prior state): Pkg.test still fails Unsatisfiable requirements detected for package ModelingToolkitBase.
  • With OrdinaryDiffEq present (master / now): identical failure.

So OrdinaryDiffEq is not the trigger. (It is also genuinely installable in the normal, non-downgrade test env — verified: Pkg.test on lib/DataDrivenLux resolves and runs with OrdinaryDiffEq v6.111.0 present.)

Real root cause (release-dependent)

The conflict is in the symbolic stack, forced by DataDrivenDiffEq's own master floor ModelingToolkit = "11.21.0" (raised in 24ae52c for Julia 1.10 precompile):

ModelingToolkit  (>= 11.21.0, DataDrivenDiffEq floor)
  -> ModelingToolkitBase >= 1.30.0      (MTK 11.21's MTKBase floor, registry compat)
       -> SymbolicUtils  >= 4.23.1      (every MTKBase >= 1.30 requires this; monotone)
but under the strict downgrade --min resolve, SymbolicUtils is held at <= 4.21.0
(Symbolics 7.0–7.21 at their floor guarantee only SymbolicUtils >= 4.21.0, and the
 pinned-to-floor Distributions caps it there), and the only SymbolicUtils-<=-4.21
 ModelingToolkitBase is <= 1.29.1 — which MTK 11.21 forbids. => no versions left.

Verified version arithmetic (live registry): MTKBase 1.30.0 → SymbolicUtils 4.23.1-4; MTKBase 1.29.1 → SymbolicUtils 4.20.1-4; MTK 11.21.0 → ModelingToolkitBase 1.30.0-1.41 (binding range); Symbolics 7.21.0 → SymbolicUtils 4.21.0-4, Symbolics 7.22.0 → SymbolicUtils 4.27.0-4.

The release this waits on

This is the broader SciML symbolic-stack downgrade-floor wall. It resolves once the downgrade --min resolve can reach SymbolicUtils >= 4.23.1 at the floor — i.e. an upstream ModelingToolkit 11.x release that raises its [compat] Symbolics floor from "7" to ">= 7.22.0" (7.22.0 being the first Symbolics whose SymbolicUtils floor, 4.27.0, satisfies the MTKBase 1.30 → SymbolicUtils >= 4.23.1 requirement that MTK 11.21 already pulls in). That aligns MTK's Symbolics floor with the SU floor its own MTKBase dependency demands.

Verified: forcing the test floor to Symbolics >= 7.22.0 (or SymbolicUtils >= 4.23.1) makes the minimal MTK-11.21 + Distributions-floor project resolve cleanly. No [compat] change in this repo can fix it without either dropping the MTK 11.21 floor (needed for 1.10 precompile) or raising DataDrivenDiffEq's own Symbolics/SymbolicUtils floors — neither is the "wait for the upstream release" path.

The downgrade-sublibraries / test (lib/DataDrivenLux) lane stays red until that ModelingToolkit release lands. That is expected and accepted; it is not hacked around.

What remains in this PR (real, release-independent, ready to merge)

  • DataDrivenSR StatsBase.coef correctness fix: getfield(x, :k) (no such field on SRResult, errored on every call) → get_parameter_values(getfield(x, :basis)).
  • Docs linkcheck: repointed dead SymbolicRegression API links to the canonical SciML-hosted docs and added the r"^https://docs\.sciml\.ai/.*" linkcheck_ignore (those pages return HTTP 403 to the linkcheck crawler but resolve in a browser).
  • DataDrivenLux Aqua/JET source fixes and the QA env [deps]/[sources] + activate_qa_env local-source develop.

All QA lanes (DataDrivenLux + DataDrivenSR, Julia 1 and lts) are green on this PR, and the revert touches only lib/DataDrivenLux/Project.toml (the test-target dep list), which is orthogonal to the qa env — so QA stays green.

Please ignore until reviewed by @ChrisRackauckas.

@ChrisRackauckas ChrisRackauckas marked this pull request as ready for review June 23, 2026 01:47
@ChrisRackauckas ChrisRackauckas merged commit 9f48529 into SciML:master Jun 23, 2026
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