Retrigger v7 outputs for 5 cancelled folders (batch 1)#1558
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These five folders had their Manifest.toml regenerated under the v7 stack in PR SciML#1551 but were cancelled by the 24h runner-queue timeout in run 25374549824 without producing artifacts. Their Manifests already resolve under DiffEqBase v7 / SciMLBase v3 / RecursiveArrayTools v4, so they should rebuild cleanly: - Testing - IntervalNonlinearProblem - NonStiffBVP - StiffBVP - NonStiffDDE This PR is a no-op apart from a comment line in each Project.toml — its sole purpose is to mark these folders as "changed" so detect-changed- benchmarks queues them for the matrix. Comments will be cleaned up in a follow-up once outputs are published, or left to be naturally removed by the next real Project.toml change. Batches are deliberately small (5 folders) to avoid resaturating the self-hosted runner queue (which is what caused the 24h cancellations last time). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
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Run 25920610513 (master push from PR #1558 merge) failed at "Detect Changed Benchmarks" with exit code 1 in ~200ms — before any visible work. Root cause: the script's curl to api.github.com/repos/SciML/SciMLBenchmarksOutput/commits has no auth header, so it uses the anonymous 60-req/hour-per-IP rate limit which is shared across all GHA runners on the same egress. When that limit is hit, the API returns a JSON error body that contains no SciMLBenchmarks.jl@<sha> pattern, the second grep -oE exits 1, pipefail propagates the failure to the LAST_BUILT_SHA assignment, and `set -e` kills the script — before it ever reaches the HEAD~1 fallback that the comment claims will catch this case. Two-part fix: (1) Pass GITHUB_TOKEN to curl as Bearer auth when present. That bumps the limit to 5000 req/hour and is per-installation, not per-IP. (2) Wrap the curl|grep|grep|head|sed pipeline in `{ ...; } || true` so a transient API hiccup or genuinely-empty output repo cleanly falls through to the HEAD~1 fallback rather than aborting the workflow. Also passes secrets.GITHUB_TOKEN to the Detect step in benchmarks.yml. The fallback path already has `|| true` on `git diff` itself, so once we reach the `if [[ -n "${LAST_BUILT_SHA}" ]]` check with an empty LAST_BUILT_SHA, the script proceeds normally on the HEAD~1 diff. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
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May 22, 2026
- Remove stale `# CI retrigger: v7 stack outputs (2026-05-15)` marker left in `Project.toml` from the batch-1 merge (SciML#1558). - Refresh `Manifest.toml` via `Pkg.update()` on Julia 1.11. Bumps: Adapt 4.5.2->4.6.0, ArrayInterface 7.24.0->7.25.0, ConcreteStructs 0.2.3->0.2.4, DifferentiationInterface 0.7.17->0.7.18, JLLWrappers 1.7.1->1.8.0, NonlinearSolveBase 2.25.0->2.26.0, RuntimeGeneratedFunctions 0.5.18->0.5.19, SafeTestsets (+0.1.0), SciMLBase 3.7.1->3.13.0, SciMLLogging 1.9.1->2.0.0, SciMLOperators 1.17.0->1.21.0, SymbolicIndexingInterface 0.3.46->0.3.48, Git_LFS_jll 3.7.0+0->3.7.1+0. - `.jmd` sources scanned: no v7 migration patterns (Bool autodiff/verbose, precs=, sol[i], ensemble prob_func arity) present; no edits needed. - Smoke-tested `weave_file(..., (:script,))` for both `simpleintervalrootfind.jmd` and `suite.jmd` -- both OK. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
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May 22, 2026
- Remove stale `# CI retrigger: v7 stack outputs (2026-05-15)` marker from Project.toml (left over from batch-1 SciML#1558 merge). - Add explicit v7 sublibrary imports needed by the benchmarks: `OrdinaryDiffEqTsit5` (Tsit5), `OrdinaryDiffEqVerner` (Vern6-9), and `OrdinaryDiffEqNonlinearSolve` (NLFunctional). DelayDiffEq no longer reexports these in v7, so the Mackey-Glass, Wheldon, and Mosquito .jmd files now `using` them explicitly. Project.toml gains matching [deps] and [compat] entries. - Refresh Manifest.toml via `Pkg.update()`. Notable bumps: DelayDiffEq 6.0.0 -> 6.0.2, DiffEqBase 7.1.0 -> 7.5.0, DiffEqDevTools 3.0.0 -> 3.1.0, LinearSolve 3.75.0 -> 3.81.0, SciMLBase 3.7.1 -> 3.13.0, OrdinaryDiffEqCore 4.0.0 -> 4.2.1, OrdinaryDiffEqDefault 2.1.0 -> 2.2.0, OrdinaryDiffEqBDF 2.0.0 -> 2.1.1, OrdinaryDiffEqRosenbrock 2.0.0 -> 2.2.0, OrdinaryDiffEqSDIRK 2.0.0 -> 2.4.0, OrdinaryDiffEqDifferentiation 3.0.0 -> 3.1.1. Smoke-tested locally: Mackey-Glass reference solve, WorkPrecisionSet across BS3/Tsit5/RK4/DP5/OwrenZen3-5/Vern6-9, and Wheldon reference solve all succeed under Julia 1.11 with the refreshed environment. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
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May 31, 2026
- Remove stale `# CI retrigger: v7 stack outputs (2026-05-15)` marker from Project.toml (left over from batch-1 SciML#1558 merge). - Add explicit v7 sublibrary imports needed by the benchmarks: `OrdinaryDiffEqTsit5` (Tsit5), `OrdinaryDiffEqVerner` (Vern6-9), and `OrdinaryDiffEqNonlinearSolve` (NLFunctional). DelayDiffEq no longer reexports these in v7, so the Mackey-Glass, Wheldon, and Mosquito .jmd files now `using` them explicitly. Project.toml gains matching [deps] and [compat] entries. - Refresh Manifest.toml via `Pkg.update()`. Notable bumps: DelayDiffEq 6.0.0 -> 6.0.2, DiffEqBase 7.1.0 -> 7.5.0, DiffEqDevTools 3.0.0 -> 3.1.0, LinearSolve 3.75.0 -> 3.81.0, SciMLBase 3.7.1 -> 3.13.0, OrdinaryDiffEqCore 4.0.0 -> 4.2.1, OrdinaryDiffEqDefault 2.1.0 -> 2.2.0, OrdinaryDiffEqBDF 2.0.0 -> 2.1.1, OrdinaryDiffEqRosenbrock 2.0.0 -> 2.2.0, OrdinaryDiffEqSDIRK 2.0.0 -> 2.4.0, OrdinaryDiffEqDifferentiation 3.0.0 -> 3.1.1. Smoke-tested locally: Mackey-Glass reference solve, WorkPrecisionSet across BS3/Tsit5/RK4/DP5/OwrenZen3-5/Vern6-9, and Wheldon reference solve all succeed under Julia 1.11 with the refreshed environment. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
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May 31, 2026
- Remove stale `# CI retrigger: v7 stack outputs (2026-05-15)` marker left in `Project.toml` from the batch-1 merge (SciML#1558). - Refresh `Manifest.toml` via `Pkg.update()` on Julia 1.11. Bumps: Adapt 4.5.2->4.6.0, ArrayInterface 7.24.0->7.25.0, ConcreteStructs 0.2.3->0.2.4, DifferentiationInterface 0.7.17->0.7.18, JLLWrappers 1.7.1->1.8.0, NonlinearSolveBase 2.25.0->2.26.0, RuntimeGeneratedFunctions 0.5.18->0.5.19, SafeTestsets (+0.1.0), SciMLBase 3.7.1->3.13.0, SciMLLogging 1.9.1->2.0.0, SciMLOperators 1.17.0->1.21.0, SymbolicIndexingInterface 0.3.46->0.3.48, Git_LFS_jll 3.7.0+0->3.7.1+0. - `.jmd` sources scanned: no v7 migration patterns (Bool autodiff/verbose, precs=, sol[i], ensemble prob_func arity) present; no edits needed. - Smoke-tested `weave_file(..., (:script,))` for both `simpleintervalrootfind.jmd` and `suite.jmd` -- both OK. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
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- Remove stale `# CI retrigger: v7 stack outputs (2026-05-15)` marker from Project.toml (left over from batch-1 #1558 merge). - Add explicit v7 sublibrary imports needed by the benchmarks: `OrdinaryDiffEqTsit5` (Tsit5), `OrdinaryDiffEqVerner` (Vern6-9), and `OrdinaryDiffEqNonlinearSolve` (NLFunctional). DelayDiffEq no longer reexports these in v7, so the Mackey-Glass, Wheldon, and Mosquito .jmd files now `using` them explicitly. Project.toml gains matching [deps] and [compat] entries. - Refresh Manifest.toml via `Pkg.update()`. Notable bumps: DelayDiffEq 6.0.0 -> 6.0.2, DiffEqBase 7.1.0 -> 7.5.0, DiffEqDevTools 3.0.0 -> 3.1.0, LinearSolve 3.75.0 -> 3.81.0, SciMLBase 3.7.1 -> 3.13.0, OrdinaryDiffEqCore 4.0.0 -> 4.2.1, OrdinaryDiffEqDefault 2.1.0 -> 2.2.0, OrdinaryDiffEqBDF 2.0.0 -> 2.1.1, OrdinaryDiffEqRosenbrock 2.0.0 -> 2.2.0, OrdinaryDiffEqSDIRK 2.0.0 -> 2.4.0, OrdinaryDiffEqDifferentiation 3.0.0 -> 3.1.1. Smoke-tested locally: Mackey-Glass reference solve, WorkPrecisionSet across BS3/Tsit5/RK4/DP5/OwrenZen3-5/Vern6-9, and Wheldon reference solve all succeed under Julia 1.11 with the refreshed environment. Co-authored-by: ChrisRackauckas-Claude <accounts@chrisrackauckas.com>
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* Refresh IntervalNonlinearProblem under v7 stack - Remove stale `# CI retrigger: v7 stack outputs (2026-05-15)` marker left in `Project.toml` from the batch-1 merge (#1558). - Refresh `Manifest.toml` via `Pkg.update()` on Julia 1.11. Bumps: Adapt 4.5.2->4.6.0, ArrayInterface 7.24.0->7.25.0, ConcreteStructs 0.2.3->0.2.4, DifferentiationInterface 0.7.17->0.7.18, JLLWrappers 1.7.1->1.8.0, NonlinearSolveBase 2.25.0->2.26.0, RuntimeGeneratedFunctions 0.5.18->0.5.19, SafeTestsets (+0.1.0), SciMLBase 3.7.1->3.13.0, SciMLLogging 1.9.1->2.0.0, SciMLOperators 1.17.0->1.21.0, SymbolicIndexingInterface 0.3.46->0.3.48, Git_LFS_jll 3.7.0+0->3.7.1+0. - `.jmd` sources scanned: no v7 migration patterns (Bool autodiff/verbose, precs=, sol[i], ensemble prob_func arity) present; no edits needed. - Smoke-tested `weave_file(..., (:script,))` for both `simpleintervalrootfind.jmd` and `suite.jmd` -- both OK. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> * Fix Bisection name ambiguity in simpleintervalrootfind.jmd The benchmark failed with: ERROR: UndefVarError: `Bisection` not defined in `Main.var"##WeaveSandBox#232"` because Roots.jl, BracketingNonlinearSolve.jl, and SimpleNonlinearSolve.jl all export `Bisection`, making the binding ambiguous after the second chunk loads BracketingNonlinearSolve/SimpleNonlinearSolve alongside the already-loaded Roots. Resolve it with an explicit `using BracketingNonlinearSolve: Bisection`, matching the workaround already used in suite.jmd. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: ChrisRackauckas-Claude <accounts@chrisrackauckas.com> Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Summary
Re-queues five benchmark folders whose Manifests resolved cleanly under the v7 stack (#1551) but which never built outputs because they were cancelled by the 24h queue-wait timeout in run 25374549824:
benchmarks/Testingbenchmarks/IntervalNonlinearProblembenchmarks/NonStiffBVPbenchmarks/StiffBVPbenchmarks/NonStiffDDEMechanism
This PR is a no-op apart from a one-line comment appended to each Project.toml. That comment is enough for
detect-changed-benchmarks.shto mark each folder as changed and queue it into the matrix.Why small batches
The previous run cancelled 27 folders because the matrix saturated the self-hosted benchmark runners and the rest of the queue exceeded the 24h queue-wait limit. Doing this in batches of ~5 keeps the queue manageable. More retrigger PRs to follow once these ones complete.
Recommended merge order
This PR's output will only auto-publish if #1556 (publish-gate fix) lands first — otherwise any single failure here will keep the whole batch's outputs from reaching SciMLBenchmarksOutput.
Note for review
Please ignore until reviewed by @ChrisRackauckas.