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Uniformize monorepo structure to OrdinaryDiffEq.jl canonical style (SciML#1220)
* Uniformize monorepo structure to OrdinaryDiffEq.jl canonical style Align Optimization.jl with the canonical OrdinaryDiffEq.jl monorepo layout: - Delete lib/OptimizationBase/test/Project.toml; fold its [deps] into the package's [extras] + [targets].test and move its [sources] (OptimizationLBFGSB, OptimizationManopt) into the main [sources] (now ../OptimizationLBFGSB / ../OptimizationManopt). Add the corresponding [compat] entries. No test/Project.toml remains anywhere (the kept test/downstream/Project.toml is a per-group sub-environment, matching the canonical pattern for special test groups). - Thread OPTIMIZATION_TEST_GROUP consistently: every lib/<X>/test/runtests.jl is now a SafeTestsets group dispatcher that reads get(ENV, "OPTIMIZATION_TEST_GROUP", "ALL") and @safetestset-includes the package's functional suite (moved to core_tests.jl) under the Core/ALL group. SafeTestsets added to each sublib's [extras]/[compat]/[targets].test. - Rewrite root test/runtests.jl as the canonical _detect_sublibrary_group dispatcher (handles bare sublib names and <sublib>_<group> suffixes, transitively develops a sublib's [sources] on Julia < 1.11, sets OPTIMIZATION_TEST_GROUP, and Pkg.tests the sublib; otherwise runs the root's own Core/GPU @safetestset groups). Fixes the previously-undefined activate_downstream_env in the GPU branch. - SublibraryCI.yml: pass group-env-name=OPTIMIZATION_TEST_GROUP and check-bounds=auto to sublibrary-project-tests.yml@v1. - DowngradeSublibraries.yml: pass group-env-name/group-env-value=Core and extend the skip list with the locally-developed in-repo sibling packages. No allow-reresolve input (removed in v1). - Add a Core-only test/test_groups.toml to every sublib so the matrix discovery declares the real group (Core on [lts,1.11,1,pre]) and does not spawn a phantom default QA-on-[1] job (no sublib has a QA suite). Root [sources] intentionally lists only OptimizationBase (the sole in-repo [deps] dependency) plus the four solver sublibraries used by the root test target; the root package re-exports only OptimizationBase, so adding the remaining sublibraries would inject false dependencies and break the true [sources] path graph. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Use canonical Title-case "All" for sublib test-group names Match OrdinaryDiffEq.jl canonical casing: the sublibrary test/runtests.jl files defaulted to and compared against the all-caps "ALL" group name. Capitalize to Title-case "All" so the group-name strings line up with the centralized matrix convention ("Core"/"QA"/test_groups.toml keys passed verbatim, capitalized). Casing-only change; dispatch logic, env var names, and fallback chains are unchanged. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * ci: canonicalize TagBot/Documentation workflows, bump downgrade Julia to 1.11 - TagBot.yml: add top-level permissions block, workflow_dispatch lookback input, root TagBot-Optimization job, and a TagBot-Subpackages matrix (fail-fast: false) over the 26 registered lib/<Name> sublibraries, each calling JuliaRegistries/TagBot@v1 with subdir: lib/<Name>. Matches OrdinaryDiffEq.jl's canonical TagBot structure. OptimizationQuadDIRECT is omitted since it is not registered in the General registry. - Documentation.yml: convert from the old inline build/deploy form to the central SciML/.github documentation.yml@v1 caller. Sublibraries resolve via the existing docs/Project.toml [sources] entries. - Downgrade.yml / DowngradeSublibraries.yml: set julia-version to 1.11. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * docs: add component READMEs to all sublibraries missing one Add lib/<Name>/README.md to the 26 sublibraries that lacked one, using the canonical OrdinaryDiffEq.jl sublibrary README template: the standard SciML badge block (Zulip, Global Docs, ColPrac, SciML Code Style) plus the "component package of Optimization.jl in the SciML ecosystem" wording with a one-line description of each package's role. SimpleOptimization already had a README and is left unchanged. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * chore: add canonical .codecov.yml and rename LICENSE to LICENSE.md Match OrdinaryDiffEq.jl's canonical monorepo layout: - Add .codecov.yml with `comment: false` to disable Codecov PR comments. - Rename the root LICENSE to LICENSE.md (content preserved via git mv). Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test: isolate root QA into canonical test/qa sub-environment Move the root package's Quality Assurance tests (Aqua + JET) into an isolated test/qa/ Project so the QA tooling dependencies no longer enter the main test target's resolve, matching the canonical OrdinaryDiffEq lib/<Name>/test/qa/ structure. - Add test/qa/Project.toml: deps Aqua, JET, Optimization, Test; [sources] Optimization = {path = "../.."}; [compat] for each + julia 1.10. - Move test/qa.jl -> test/qa/qa.jl (Aqua + JET tests preserved verbatim; add `using Test` so the file is self-contained in the isolated env). - runtests.jl: add activate_qa_env() (Pkg.activate(test/qa) + instantiate, plus develop-by-path on Julia < 1.11 where [sources] is ignored). The QA safetestset now runs last in the Core group after activating the qa env, so the main-environment tests above are unaffected. CI dispatches only GROUP=Core, so QA continues to run exactly as before. - Remove Aqua and JET from the main Project.toml [extras], [targets].test, and [compat]; they now live solely in the qa environment. Verified on Julia 1.11 in an isolated depot: the qa env instantiates and resolves (Aqua 0.8.16, JET 0.9.20, Optimization 5.6.1 via ../.., Test 1.11.0); the Aqua testset runs green (10/10 pass). No sublibrary runs QA today (the three that list Aqua in [extras] never call it), so per the preserve-existing-behavior rule none were given a qa env. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test: align sublibrary test_groups.toml version matrix to canonical base set Set every lib/*/test/test_groups.toml [Core] group to the canonical base/standard version matrix ["lts", "1", "pre"], dropping the redundant "1.11" entry so the standard test matrix matches the uniform monorepo contract (base = lts/1/pre). Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * test: split root QA into its own dep-adding group (excluded from Core) Make the root package follow the canonical group-folder contract: - runtests.jl: QA (Aqua + JET, isolated test/qa environment) was running inside the Core/All block, which both pulled the isolated qa env into the base run and ran QA on the Core version matrix. Move it into its own `GROUP == "QA"` branch so the base/Core run stays in the main test env and QA runs only when its group is selected. - Add root test/test_groups.toml declaring Core (lts/1/pre), QA (lts/1), and GPU (1, self-hosted) with the canonical version matrix. - CI.yml: run Core on [lts, 1, pre] and QA on [lts, 1] via a group/version matrix instead of a single hardcoded Core/[1.11, lts] job. Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * ci: canonical TagBot thin caller + downgrade skip cleanup Convert TagBot.yml from the inline JuliaRegistries/TagBot form to the canonical SciML/.github tagbot.yml@v1 thin caller, with a tagbot-subpackages matrix over the 26 registered lib/* sublibraries (OptimizationQuadDIRECT excluded: not registered in General). Reduce the downgrade callers' skip lists to only the genuine non-stdlib, non-sublib extra (SymbolicAnalysis); stdlibs and in-repo sublibraries are now auto-populated by the centralized downgrade workflows. Move julia-version from 1.11 to lts (the minimum-supported floor). Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com> 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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‎.codecov.yml‎

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‎.github/workflows/CI.yml‎

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include:
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version: "1"
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group: "${{ matrix.group }}"
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coverage-directories: "src,lib/OptimizationBase/src,lib/OptimizationBBO/src,lib/OptimizationCMAEvolutionStrategy/src,lib/OptimizationEvolutionary/src,lib/OptimizationGCMAES/src,lib/OptimizationIpopt/src,lib/OptimizationMadNLP/src,lib/OptimizationManopt/src,lib/OptimizationMOI/src,lib/OptimizationMetaheuristics/src,lib/OptimizationMultistartOptimization/src,lib/OptimizationNLopt/src,lib/OptimizationNOMAD/src,lib/OptimizationOptimJL/src,lib/OptimizationOptimisers/src,lib/OptimizationPolyalgorithms/src,lib/OptimizationQuadDIRECT/src,lib/OptimizationSpeedMapping/src"
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run: julia --project=docs/ -e 'using Pkg; Pkg.develop(vcat(PackageSpec(path = pwd()), [PackageSpec(path = joinpath("lib", dir)) for dir in readdir("lib") if (dir !== "OptimizationMultistartOptimization")])); Pkg.instantiate()'
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‎.github/workflows/Downgrade.yml‎

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‎.github/workflows/DowngradeSublibraries.yml‎

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skip: "SymbolicAnalysis"
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‎.github/workflows/SublibraryCI.yml‎

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‎Project.toml‎

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test = ["BenchmarkTools", "Boltz", "ComponentArrays", "DiffEqFlux", "Enzyme", "FiniteDiff", "Flux", "ForwardDiff", "Ipopt", "IterTools", "LinearSolve", "Lux", "MLUtils", "ModelingToolkit", "Optim", "OptimizationLBFGSB", "OptimizationMOI", "OptimizationOptimJL", "OptimizationOptimisers", "OrdinaryDiffEqTsit5", "Pkg", "Random", "ReverseDiff", "SafeTestsets", "SciMLSensitivity", "SparseArrays", "Symbolics", "Test", "Tracker", "Zygote", "Mooncake", "SciMLLogging"]

‎lib/OptimizationAuglag/Project.toml‎

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test = ["Test", "ForwardDiff", "MLUtils", "OptimizationOptimisers", "Random", "SafeTestsets"]

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