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Uniformize monorepo structure to OrdinaryDiffEq canonical style#13

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ChrisRackauckas merged 12 commits into
SciML:mainfrom
ChrisRackauckas-Claude:uniformize-monorepo-structure
Jun 8, 2026
Merged

Uniformize monorepo structure to OrdinaryDiffEq canonical style#13
ChrisRackauckas merged 12 commits into
SciML:mainfrom
ChrisRackauckas-Claude:uniformize-monorepo-structure

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@ChrisRackauckas-Claude ChrisRackauckas-Claude commented Jun 7, 2026

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This PR fully uniformizes the repository to the OrdinaryDiffEq.jl canonical monorepo style.

Canonicalization done

Root track

  • Converted the bare [workspace] root into a real package Project.toml (name/uuid/version, [deps]+[sources] to lib/<Name>, [compat], [extras]+[targets].test). The umbrella now @reexports OUQBase, making it a buildable, meaningful package and giving a traversable [sources] path graph for sublibrary matrix discovery.
  • Added a GROUP-dispatched root CI.yml (matrix over the root's own Core group on lts/1.11/1/pre; no hardcoded sublibrary GROUP rows — sublibs are covered by the SublibraryCI project model).
  • Added a root Downgrade.yml calling downgrade.yml@v1 (no allow-reresolve).
  • Added root test/runtests.jl with a _detect_sublibrary_group dispatcher: if GROUP names lib/<X> it activates that sublib, develops its [sources] on Julia < 1.11, sets OPTIMALUNCERTAINTYQUANTIFICATION_TEST_GROUP, and Pkg.tests it; otherwise it runs the root's own @safetestset groups (umbrella-load smoke test).

Sublibraries

  • Deleted lib/CanonicalMoments/test/Project.toml and lib/OUQBase/test/Project.toml; folded their deps into [extras] + [targets].test of each package Project.toml.
  • Removed OUQBase's [workspace] test-subproject wiring.
  • Dropped TestItemRunner from CanonicalMoments test deps (unused; tests already use SafeTestsets).
  • Rewrote every sublib test/runtests.jl to read OPTIMALUNCERTAINTYQUANTIFICATION_TEST_GROUP and @safetestset-include per group (Core), mirroring OrdinaryDiffEq sublib runtests. DiscreteMeasures' test body moved to discrete_measures_tests.jl so its runtests is a pure dispatcher.

Workflows

  • SublibraryCI.yml: added with: { group-env-name: OPTIMALUNCERTAINTYQUANTIFICATION_TEST_GROUP, check-bounds: auto }.
  • DowngradeSublibraries.yml: added group-env-name/group-env-value: Core, skip list of siblings (CanonicalMoments,DiscreteMeasures,OUQBase) + stdlibs; auto-discovers lib/*.
  • dependabot.yml: dropped the removed test/ subprojects.

The chosen group-env-name OPTIMALUNCERTAINTYQUANTIFICATION_TEST_GROUP is threaded consistently: caller workflows == every sublib runtests == the root dispatcher.

Verified locally (isolated depot, Julia 1.11.9)

  • TOML-parsed every changed Project.toml; confirmed every [targets].test dep appears in [extras].
  • Confirmed zero test/Project.toml, zero @testitem/ReTestItems/TestItemRunner, zero [workspace] remain; no @test_broken/@test_skip added; no [compat] floor lowered (all julia floors 1.10).
  • YAML-parsed all four changed/added workflows.
  • Instantiated the root umbrella and two representative sublibs (DiscreteMeasures, CanonicalMoments).
  • Ran the new @safetestset dispatch for two sublib Core groups:
    • DiscreteMeasures Core: Discrete Measures | 45 45 passed.
    • CanonicalMoments Core: Orthogonal Polynomial Roots | 11 11 and Moment Sequence | 260 260 passed.
  • Ran the root's smallest group via Pkg.test() with GROUP=Core: Umbrella Load | 5 5 passed.
  • Exercised the root dispatcher end-to-end with GROUP=DiscreteMeasures: it activated lib/DiscreteMeasures and ran its suite (45 45 passed).
  • Ran Runic on all changed/added .jl files (idempotent, clean).

What CI must confirm

  • The OUQBase Core group (Flood Problem solve) on the full matrix — locally OUQBase pulls the ModelingToolkit/Optimization stack; its group was not run end-to-end here, only instantiated transitively via the root. CI's SublibraryCI project model will run it.
  • Downgrade resolution for all three sublibs and the root on the floor versions.
  • Behavior on Julia LTS (1.10) and pre.

Ignore until reviewed by @ChrisRackauckas.

🤖 Generated with Claude Code

ChrisRackauckas and others added 12 commits June 7, 2026 16:15
@ChrisRackauckas @claude
Uniformize monorepo structure to OrdinaryDiffEq canonical style
fbc8d6a 
Make the repo match the OrdinaryDiffEq.jl canonical monorepo invariants:

Root track:
- Convert the bare [workspace] root into a real package Project.toml
  (name/uuid/version, [deps]+[sources] to lib/<Name>, [compat],
  [extras]+[targets].test). The umbrella now @reexport-s OUQBase so it
  is a buildable, meaningful package and the [sources] path graph is
  traversable by sublibrary matrix discovery.
- Add a GROUP-dispatched root CI.yml (matrix over the root's own Core
  group; no hardcoded sublibrary rows) and a root Downgrade.yml calling
  downgrade.yml@v1 (no allow-reresolve).
- Add root test/runtests.jl with a _detect_sublibrary_group dispatcher:
  if GROUP names lib/<X> it activates and Pkg.test-s that sublib under
  OPTIMALUNCERTAINTYQUANTIFICATION_TEST_GROUP; otherwise runs the root's
  own @safetestset groups (umbrella load smoke test).

Sublibraries:
- Delete lib/CanonicalMoments/test/Project.toml and
  lib/OUQBase/test/Project.toml; fold their deps into [extras] +
  [targets].test in each package Project.toml.
- Remove OUQBase's [workspace] test-subproject wiring.
- Drop TestItemRunner from CanonicalMoments test deps (unused).
- Rewrite every sublib test/runtests.jl to read
  OPTIMALUNCERTAINTYQUANTIFICATION_TEST_GROUP and @safetestset-include
  per group (Core), mirroring OrdinaryDiffEq sublib runtests.

Workflows:
- SublibraryCI.yml: thread group-env-name
  OPTIMALUNCERTAINTYQUANTIFICATION_TEST_GROUP + check-bounds: auto.
- DowngradeSublibraries.yml: add group-env-name/group-env-value Core,
  skip list of siblings + stdlibs; auto-discovers lib/*.
- dependabot.yml: drop the removed test/ subprojects.

No [compat] floors lowered; no tests skipped/broken/loosened.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ChrisRackauckas @claude
Use canonical capitalized test-group names in sublib runtests
efc619e 
Match SciML/OrdinaryDiffEq.jl casing: the sublibrary test/runtests.jl
default group and comparison strings used all-caps "ALL"; canonicalize
to Title-case "All" so they line up with the umbrella runner, which
passes "Core"/"All" verbatim through OPTIMALUNCERTAINTYQUANTIFICATION_TEST_GROUP.

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>
@ChrisRackauckas @claude
Add canonical config files, LICENSE.md renames, and fix typos
ed1b238 
Rename LICENSE->LICENSE.md (root + add to 3 sublibs), rename
_typos.toml->.typos.toml with [default.extend-words], add .codecov.yml
(comment:false), and complete .gitignore to match OrdinaryDiffEq canonical
form. Fix genuine source/comment typos surfaced by typos so SpellCheck stays
green without silencing real misspellings.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ChrisRackauckas @claude
Add sublibrary READMEs and test_groups.toml
4995225 
Add canonical component READMEs (Zulip + Global Docs + ColPrac + SciML Style
badges, "component of the OptimalUncertaintyQuantification.jl monorepo"
wording) to each lib/* sublibrary, and declare each sublibrary's real test
groups in test/test_groups.toml. All three sublibraries only have a Core
group (no QA/Aqua tests exist), tested across lts/1.11/1/pre.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ChrisRackauckas @claude
Add Documentation, DocPreviewCleanup, Downstream workflows and TagBot…
f6db09e 
… root job

Add the central @v1 Documentation.yml and DocPreviewCleanup.yml callers and a
canonical IntegrationTest (Downstream.yml) matching OrdinaryDiffEq's embedded
form (empty matrix no-op until registered downstream consumers exist). Add the
root TagBot-OptimalUncertaintyQuantification job alongside the existing
subpackages matrix to match the canonical TagBot structure.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ChrisRackauckas @claude
Canonicalize root CI cache/env and add umbrella docs wiring
3af232d 
Add event-split Julia depot cache (push read+write, PR restore-only with
matching restore-keys) and the JULIA_DEPOT_PATH pin to the root CI.yml to
match OrdinaryDiffEq's canonical CI. Add umbrella docs/ wiring: docs/Project.toml
(umbrella + sublibraries via [sources] with [compat]), docs/make.jl, docs/pages.jl,
and docs/src/index.md.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ChrisRackauckas @claude
Add missing [compat] bounds to sublibrary deps
c0cf757 
Add ADD-only [compat] entries for previously unbounded dependencies:
CanonicalMoments weakdeps ChainRulesCore ("1") and ForwardDiff ("0.10, 1");
OUQBase deps CanonicalMoments/DiscreteMeasures ("0.1"), Optimization ("5"),
PolynomialRoots ("1"), and SymbolicUtils ("3"). Bounds are set at or below the
versions the umbrella and sublibrary test targets currently resolve (verified by
instantiate/resolve on Julia 1.11), so no existing resolve is constrained out and
no floor is lowered. CanonicalMoments Core tests pass (271/271) under the new bounds.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ChrisRackauckas @claude
Ensure docs assets dir exists before copying Project.toml
caf4395 
mkpath the docs/src/assets directory in make.jl before cp so the documentation
build does not error when the directory is absent.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ChrisRackauckas @claude
test: move tests into canonical test/<Group>/ folders (Core)
f012429 
Restructure the root umbrella test and all three sublibrary test suites
(CanonicalMoments, DiscreteMeasures, OUQBase) into per-group test/<Group>/
folders, matching the OrdinaryDiffEq/NonlinearSolve canonical GROUP-FOLDER
layout. Every test now lives in exactly one group folder:

  - test/Core/umbrella_load.jl
  - lib/CanonicalMoments/test/Core/{orthopoly_roots,moment_sequence,stenger_setup}.jl
  - lib/DiscreteMeasures/test/Core/discrete_measures_tests.jl
  - lib/OUQBase/test/Core/FloodProblem/*.jl

All include() paths in the dispatchers are updated to the Core/ prefix.
No tests are added, removed, skipped, or loosened; the same @safetestset
set runs from the new paths. All sublibs run only the Core group (no QA
tools / no dep-adding groups), so no per-group Project.toml is needed and
Core remains part of the base/All run.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ChrisRackauckas @claude
ci: normalize Core version matrix to [lts, 1, pre]; finish Core/ incl…
7fa9273 
…ude paths

Drop the non-canonical "1.11" entry from every sublibrary's [Core] test group
(CanonicalMoments, DiscreteMeasures, OUQBase) and from the root CI.yml version
matrix, so the base/Core groups run the canonical [lts, 1, pre] set matching the
OrdinaryDiffEq/NonlinearSolve monorepo convention. There are no dep-adding,
QA, or GPU groups in this repo, so no group is excluded from All and no
per-group Project.toml or runner matrix is introduced.

Also completes the test/<Group>/ restructuring by updating the include() paths
in each runtests.jl dispatcher to the Core/ prefix (the prior commit moved the
files but the path edits land here). No tests are added, removed, skipped, or
loosened; no compat floors are lowered.

Verified with the centralized compute_affected_sublibraries.jl --projects-matrix
script: it emits exactly Core on [lts, 1, pre] for each of the three sublibs.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ChrisRackauckas @claude
test(OUQBase): wire previously-orphaned FloodProblem tests into Core …
d07db6d 
…group

The OUQBase test/runtests.jl only ever included Core/FloodProblem/Q_only.jl;
the other four flood-problem files were unreachable since before the monorepo
restructure (orphaned upstream). 2D_independent.jl, full_independent.jl, and
full_dependent.jl only build OUQSystem fixtures (pushed into Main-scoped
problem dictionaries via `isdefined(Main, ...)` guards), and
test_canonical_moments.jl consumed those dictionaries through an
`include` of a Problems/all_problems.jl aggregator that never existed in the
repo (and whose relative path was off by one directory level).

Reconstruct the missing test/Problems/all_problems.jl fixture aggregator: it
defines the eight problem dictionaries and includes each FloodProblem setup
file so they populate it. Fix the include path in test_canonical_moments.jl to
reach the aggregator under the new test/Core/ layout, and run both the Q-only
smoke solve and the canonical-moments objective assertion at top level in Main
(so the Main-scoped fixture dictionaries are visible). Guard Q_only.jl's
expensive trailing solve behind a LOAD_OUQ_PROBLEMS_FIXTURE flag so it runs
once from its own group entry rather than again when loaded as a fixture.

The canonical-moments objective test (@test isapprox(obj_val, 0.6897,
atol=0.01)) now runs and passes; all four formerly-orphaned files are exercised
as part of the Core group that the sublibrary CI matrix runs on [lts, 1, pre].

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ChrisRackauckas @claude
CI: canonical TagBot thin caller + downgrade-caller cleanup
0a04d7c 
Replace the verbose TagBot.yml with the canonical SciML thin caller
(tagbot.yml@v1). The tagbot-subpackages matrix is omitted because none
of the lib/ sublibraries (CanonicalMoments, DiscreteMeasures, OUQBase)
are registered in the General registry yet, and TagBot errors on
unregistered subdirs.

Remove the hand-listed skip: inputs (stdlibs + in-repo sublibs) from
the Downgrade.yml and DowngradeSublibraries.yml callers; the centralized
workflows now auto-populate skip. Drop julia-version: "1.10" to take the
central 'lts' default (the minimum-supported floor).

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
@ChrisRackauckas ChrisRackauckas marked this pull request as ready for review June 8, 2026 09:30
@ChrisRackauckas ChrisRackauckas merged commit b4b1979 into SciML:main Jun 8, 2026
10 of 11 checks passed
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@ChrisRackauckas-Claude @ChrisRackauckas