Document public developer APIs

[ChrisRackauckas-Claude]

Ignore this PR until reviewed by @ChrisRackauckas.

Summary

• Add a public developer API reference page for public monorepo/lib APIs.
• Add concise source docstrings for public developer API names rendered on the page.
• Run Runic formatting for the repo before committing.

Verification

• Targeted lib public-name scanner reported public name count: 298, gap count: 0.
• timeout 3600 /home/crackauc/.juliaup/bin/julia +release --project=docs -e 'using Pkg; Pkg.instantiate(); include("docs/make.jl")' exited 0 after final formatting.\n- rg 'no docs found for' ordinary_docs_precommit.log returned no matches before the generated log was removed.\n- timeout 3600 /home/crackauc/.juliaup/bin/julia +release --project=/home/crackauc/sandbox/tmp_20260708_051717_3275/.runic_env -m Runic --check . exited 0.\n- git diff --check exited 0.

[ChrisRackauckas-Claude]

Update after source-site docstring pass.

Changes pushed:

• Rebased on current origin/master (b797bac).
• Moved the public API docstrings out of the temporary public_api_docstrings.jl files and onto the source/original definitions.
• Deleted the centralized public_api_docstrings.jl files.
• Added fuller SciMLStyle-style docs/examples for the more user-facing APIs touched here, including nonlinear solver wrappers and AMF construction.

Current branch tip: 3a0d70c

Verification run locally:

• git diff --check origin/master...HEAD: passed.
• timeout 3600 /home/crackauc/.juliaup/bin/julia +release --project=/home/crackauc/sandbox/tmp_20260708_051717_3275/.runic_env -m Runic --check .: passed.
• timeout 3600 /home/crackauc/.juliaup/bin/julia +release --project=docs -e 'using Pkg; Pkg.instantiate(); include("docs/make.jl")': exited 0 after rebase. Existing unrelated docs warnings remain.\n- Parsed docs log for missing docs/src/devtools/internals/public_api.md entries: 0.\n- timeout 3600 /home/crackauc/.juliaup/bin/julia +release --project=. -e 'using Pkg; Pkg.test()': timed out at 1 hour, no assertion failure observed before timeout.\n- Retried with timeout 7200 /home/crackauc/.juliaup/bin/julia +release --project=. -e 'using Pkg; Pkg.test()': timed out after 2 hours in test/Integrators_II/resize_tests.jl:231. Many groups passed before timeout, including Export tests, Alg Events Tests, Reverse Directioned Event Tests, Step Limiter Tests, and others. This is a timeout, not a test assertion failure.\n\nIgnore until reviewed by @ChrisRackauckas.

[ChrisRackauckas-Claude]

Follow-up on current CI failures:

The downgrade-sublibraries workflow is currently reporting failures for lib/OrdinaryDiffEqAMF and lib/OrdinaryDiffEqCore, but GitHub is not exposing job logs yet because the workflow is still in progress. I ran the corresponding normal sublibrary Core test groups locally on the rebased branch with Julia 1.11:

• ODEDIFFEQ_TEST_GROUP=Core timeout 3600 /home/crackauc/.juliaup/bin/julia +1.11 --project=lib/OrdinaryDiffEqCore -e 'using Pkg; Pkg.test()': passed. Groups observed: Sparse isdiag Performance 10/10, Algebraic Vars Detection 15/15, Discontinuity Detection 30/30.\n- ODEDIFFEQ_TEST_GROUP=Core timeout 3600 /home/crackauc/.juliaup/bin/julia +1.11 --project=lib/OrdinaryDiffEqAMF -e 'using Pkg; Pkg.test()': passed. OrdinaryDiffEqAMF 24/24.\n\nSo the current CI failures appear specific to the downgrade workflow setup rather than the normal sublibrary tests. I will need the failed job logs after the workflow completes to diagnose the downgrade-specific failure precisely.

[ChrisRackauckas-Claude]

Update pushed: 0b8852b49 (Split user and developer API docs).

What changed in this update:

• Split user-facing API docs into docs/src/api/diffeqbase.md and docs/src/api/ordinarydiffeqcore.md.
• Retitled the old mixed page as Developer Extension API with an explicit warning that it is not application/user API.
• Removed OrdinaryDiffEq cache supertypes/concrete caches from public declarations/rendered docs; they remain internal implementation details.
• Removed handle_callback_modifiers! from public/rendered docs.
• Narrowed OrdinaryDiffEqNonlinearSolve public API to NLFunctional, NLAnderson, and NLNewton; removed internal nonlinear-solver helpers from public/docs.
• Removed OrdinaryDiffEqDifferentiation public API declarations/docs.
• Converted a large set of new simple @doc "..." name attachments in Core/DiffEqBase slices back to definition-site docstrings.

Local verification:

• git diff --check: passed.
• timeout 3600 julia +release --project=/home/crackauc/sandbox/tmp_20260708_051717_3275/.runic_env -m Runic --check .: passed.
• timeout 3600 julia +release --project=docs -e 'using Pkg; Pkg.instantiate(); include("docs/make.jl")': exited 0. The edited public API pages no longer report missing-doc warnings. Remaining warnings are pre-existing docs warnings in tableaus/TaylorSeries/misc, HTML size warnings, and private/internal docstrings not included in the manual.
• Targeted Julia public/private classification check: passed. Confirmed cache supertypes, @cache, handle_callback_modifiers!, nonlinear solve internals, differentiation internals, and SDIRK caches are not public; NLFunctional, NLAnderson, NLNewton, and ImplicitEulerESDIRKIMEXTableau are public.

Known local test failure:

• timeout 3600 julia +release --project=lib/OrdinaryDiffEqCore -e 'using Pkg; Pkg.test()' fails in QA all_explicit_imports_are_public because AbstractSciMLOperator is imported from SciMLOperators but is not public there:
  AbstractSciMLOperator is not public in SciMLOperators but it was imported from SciMLOperators at lib/OrdinaryDiffEqCore/src/OrdinaryDiffEqCore.jl:40:24.
• AllocCheck and JET sections passed before that QA failure (Core Infrastructure AllocCheck Tests: 1 pass; JET Tests: 30 pass, 1 broken).
• I started a separate investigation agent to reproduce this on the unmodified base branch and identify/report the underlying commit, per repo instructions.

Ignore until reviewed by @ChrisRackauckas.

[ChrisRackauckas-Claude]

Rebased on current origin/master after #3833 and force-pushed with lease. New tip: 924b9238d. Re-ran git diff --check and the targeted public/private classification check after rebase; both passed.

[ChrisRackauckas-Claude]

Pushed follow-up commits through 6a19c6f57.

What changed since the earlier split:

• Restored abstract cache supertypes as developer extension API while keeping concrete cache structs private/internal.
• Made OrdinaryDiffEqCore.@cache, perform_step!, _resolved_QT, and PredictiveControllerCache developer-public and documented them on the developer API page.
• Kept postamble! non-public in OrdinaryDiffEqCore; it is owned by SciMLBase and is not a Core-owned developer API.
• Restored lower-level OrdinaryDiffEqNonlinearSolve hooks used by SDIRK as developer-public (build_nlsolver, nlsolve!, nlsolvefail, markfirststage!, du_alias_or_new, initial_η, compute_step!, anderson, anderson!) and documented them separately from the user-facing NL* algorithms.
• Restored shared OrdinaryDiffEqDifferentiation Jacobian/linear-solve utilities as developer-public (build_J_W, build_jac_config, calc_J, calc_J!, dolinsolve, islinearfunction) and documented them on the developer page.
• Added missing API coverage for DiffEqBase.DEVerbosity, DiffEqBase.initialize!, DiffEqBase.finalize!, OrdinaryDiffEqCore.Predictor, and ssp_coefficient.
• Removed duplicate rendered docs entries for CompositeAlgorithm and DEVerbosity.

Local verification run:

• git diff --check: passed
• Runic: passed
• targeted Base.ispublic classification check: passed (@cache, perform_step!, nonlinear-solve hooks, and differentiation shared hooks public; concrete caches, handle_callback_modifiers!, postamble!, jacobian!, update_W!, ESDIRKIMEXCache private)
• docs build: passed; filtered check found no duplicate/no-docs warnings from the edited API pages after the final cleanup
• Pkg.test() for OrdinaryDiffEqFunctionMap: passed
• Pkg.test() for OrdinaryDiffEqLinear: passed

Known non-branch failures/limitations:

• OrdinaryDiffEqCore QA still fails on clean base with registered SciMLOperators v1.23.0 because AbstractSciMLOperator is not public there. A subagent reproduced that on clean origin/master and verified it passes when SciMLOperators is developed to current master, where the public declaration already exists. This needs a SciMLOperators release/tag, not an OrdinaryDiffEq PR change.
• OrdinaryDiffEqSDIRK local Pkg.test() did not reach QA assertions; it errored during QA environment instantiate with a Pkg manifest assertion (entry.tree_hash !== nothing && entry.path !== nothing). I cleaned up the Pkg-generated test environment mutations afterward.

Ignore this PR until reviewed by @ChrisRackauckas.

[ChrisRackauckas-Claude]

Pushed another controller-interface slice in a079f94de.

What changed:

• Expanded OrdinaryDiffEqCore controller interface docstrings into SciMLStyle-style sections: Arguments, Keywords, Returns, Fields, Interface, and Interface Rules where applicable.
• Removed the copied @doc (@doc ...) pattern from the controller knob accessors and gave each accessor its own docstring.
• Added a rendered controller interface contract to docs/src/api/controllers.md describing descriptor/cache separation, resolved CommonControllerOptions, divisor semantics, accept/reject/reinit rules, and cache non-user-API status.
• Added a generic custom-controller conformance test in test/InterfaceI/controllers.jl that solves with a third-party AbstractController, exercises setup_controller_cache, stepsize_controller!, step_accept_controller!, step_reject_controller!, get_EEst/set_EEst!, knob accessors, and reinit_controller! through the public hooks.
• Declared the controller defaults and documented selectable algorithm-integrated controllers public where the docs already render them: qmax_first_step_default, failfactor_default, BDFController, JVODEController, ExtrapolationController, and KantorovichTypeController.

Local verification run:

• git diff --check passed.
• Runic check on touched Julia files passed.
• Focused controller test passed in a temp local env with repo/Core/LowStorage developed: qmax_first_step 21/21 and generic controller interface 13/13.
• Public declaration smoke test passed with Base.ispublic for the six newly aligned symbols.
• docs/make.jl completed successfully after qualifying new controller-page refs. It still emits existing unrelated warnings from tableau/Taylor/misc docs and the existing not-in-manual list, but no controller-page cross-reference errors remain.

Still not claiming the whole repo-wide objective is done. Parallel audits found remaining gaps in Core algorithm/cache/nonlinear/dense/integrator hook docstrings and exported solver algorithm docstrings; those need follow-up slices.

[ChrisRackauckas-Claude]

Pushed another focused interface-doc slice in 0d324c436.

What changed:

• Expanded OrdinaryDiffEqCore algorithm hierarchy docstrings into sectioned developer-interface docs for ODE, adaptive, composite, stochastic/RODE, implicit/Newton/Rosenbrock, exponential, Adams variable-order, DAE, partitioned, and second-order families.
• Expanded OrdinaryDiffEqCache, OrdinaryDiffEqConstantCache, OrdinaryDiffEqMutableCache, get_fsalfirstlast, and alg_cache docs with explicit interface rules about cache construction, perform_step!, FSAL storage, SciMLBase cache participation, and concrete cache non-user-API status.
• Expanded the StochasticDiffEq cache supertypes in the same shared Core file with the same developer-public cache rules.
• Extended test/InterfaceI/public_api_package_split.jl to exercise split-package algorithms through public integrator hooks only: init, set_proposed_dt!, step!, interpolation call syntax, get_du!, solve!, successful_retcode, and final solution accuracy, without importing or inspecting concrete cache types.

Local verification:

• git diff --check passed.
• Runic check passed on touched files.
• test/InterfaceI/public_api_package_split.jl passed in a temp local env with repo/split packages developed: 59/59.
• docs/make.jl completed successfully. It still emits the same unrelated tableau/Taylor/misc warnings and size warnings seen before, but no new Core interface doc errors.

Still not claiming the full repo-wide objective is complete; remaining audit targets include nonlinear-solver hooks, dense interpolation hooks, many algorithm trait hooks, and exported solver algorithm docstrings.

[ChrisRackauckas-Claude]

Pushed d9cd84a5d to document the nonlinear solver developer interface and replace cache-field assertions in linear_nonlinear_tests.jl with public behavior checks.

Changes in this slice:

• Expanded the Core nonlinear solver developer API docstrings at the definition points for AbstractNLSolverCache, AbstractNLSolverAlgorithm, AbstractNLSolver, W/J freshness hooks, and resize hooks.
• Replaced direct integ.cache.nlsolver.cache.weight assertions with checks through public solver behavior: solve, init, step!, solve!, successful_retcode, sol.stats.nw, and accuracy against the matrix exponential.

Local checks run:

• Runic.main --check lib/OrdinaryDiffEqCore/src/OrdinaryDiffEqCore.jl lib/OrdinaryDiffEqNonlinearSolve/test/linear_nonlinear_tests.jl passed.
• Targeted include of lib/OrdinaryDiffEqNonlinearSolve/test/linear_nonlinear_tests.jl in a temp env with local OrdinaryDiffEqNonlinearSolve, OrdinaryDiffEqSDIRK, OrdinaryDiffEqBDF, and OrdinaryDiffEqRosenbrock passed on Julia 1.10.
• Docs build with julia +release --project=docs -e 'using Pkg; Pkg.instantiate(); include("docs/make.jl")' completed successfully, with existing unrelated Documenter warnings.\n\nPackage-level note:\n- Pkg.test() for lib/OrdinaryDiffEqNonlinearSolve fails before this PR-specific test logic under the package env due to dependency/precompile errors. I reproduced a base-branch failure on origin/master at 342617a63: find_algebraic_vars_eqs undefined while precompiling OrdinaryDiffEqNonlinearSolve, cascading into OrdinaryDiffEqSDIRK, OrdinaryDiffEqBDF, and OrdinaryDiffEqFIRK. I will route that as a separate base-branch investigation as soon as an agent slot frees.