[Jammy2211]

Summary

Phase A3 of the search-extensibility epic (PyAutoFit#1677), stacked on #1679 (A2): this PR's base is feature/search-ext-a2-objective-bridge; merge #1679 first and GitHub retargets this one to main. Six A3 commits plus a merge of A2 and one reconciliation commit.

Phase A3 builds on A2's run(ctx) bridge. It replaces A2's provisional samples types with the single samples adapter (autofit/non_linear/samples/adapter.py: RawSamples, samples_from_raw, one log-prior helper, sentinel recognition without rewriting, ChainPosterior.thin shared by Emcee, Zeus and NUTS with the empty-chain fallback). Every search implements one raw_samples_from; samples_via_internal_from is written once on NonLinearSearch. Byte-identical golden samples.csv fixtures (generated on main, their own first commit) cover Emcee, Dynesty, Nautilus, NUTS and SMC. A search's archive (checkpointer: DillCheckpointer, PickleCheckpointer for NUTS/SMC, NativeFileCheckpointer for emcee HDF / dynesty savestate / nautilus hdf5 / NSS pkl; atomic writes, retain_after_completion) is separated from its resume_state, with corruption and retention precedence in docs/design/checkpointing.md (D5); a completed Dynesty folder keeps what it needs to reload. Constructing Emcee, BlackJAXNUTS or SMC no longer mutates conf.instance. Pre-A3 output folders load through format-aware legacy detection (the HDF probe moved, not replaced); loading is injected for directory, database (no-op), null, zipped and summary-only paths. FitContext.checkpointer and FitContext.resume are now wired from these strategies and docs/design/run_ctx.md Revision 1 says so. --auto run at effective level safe; tier judge → human /prm.

Strict xfails: 9 → 4. Deleted (now passing): the three CONFIG_MUTATION_XFAIL (Emcee, BlackJAXNUTS, SMC) and the two Dynesty DISK_INTERNAL_XFAIL. The four import-time AutoCorrelationsSettings xfails are A4's and stay strict. Golden identifiers unchanged.

API Changes

Added autofit.non_linear.samples.adapter (RawSamples with optional log_prior/samples_kwargs/label, samples_from_raw, log_prior_list_from, is_invalid/invalid_count, INVALID_SENTINELS, ChainPosterior), autofit.non_linear.checkpoint (DillCheckpointer(strip_attributes=), PickleCheckpointer, NativeFileCheckpointer(filename, loader) with save/load/exists/finalize/discard, retain_after_completion, path; load_legacy_search_internal, checkpointer_kind), NonLinearSearch.{checkpointer,resume_state,samples_cls,raw_samples_from,load_search_internal,retains_search_internal}, the checkpointer manifest capability (dill | pickle | native:<file>; schema-compatible addition; generated docs gain an "Archive" column), paths.stores_search_internal (False for NullPaths/DatabasePaths). Changed: concrete searches implement raw_samples_from instead of samples_via_internal_from (direct overrides still work); Emcee/NUTS/SMC keep their archive regardless of config; a completed Dynesty folder loads from dill, savestate only for an unfinished run; NUTS/SMC write no pickle on DatabasePaths; Emcee gains the empty-chain fallback and Zeus applies it in test mode; Zeus computes autocorrelations once per conversion; Nautilus's resume loader raises NotImplementedError (nautilus reopens its own file); base info_from returns {}. resumable values unchanged (Zeus stays False; resume not proven).
See full details below.

Test Plan

• Full pytest test_autofit -x on the integrated head: 3531 passed, 1 skipped, 4 xfailed
• Goldens byte-identical after every commit; test_adapter, test_checkpoint ×2, test_search_internal_loading, test_fit_context, plus A2's probe/timing/make_fitness/BFGS tests: 117 passed
• nojax emulation test_autofit/non_linear: 1253 passed, 136 skipped, 2 xfailed; import autofit loads no optional backend
• Fresh process: af.Emcee(), af.BlackJAXNUTS(), af.SMC() leave conf.instance["output"]["search_internal"] unchanged (re-run by the reviewer)
• afT {Emcee,Zeus,DynestyStatic,Nautilus,Nautilus_jax,Drawer,SMC}.py under test mode exit 0 (BlackJAXNUTS and MultiStartResurrect fail their own asserts identically on main)
• Nautilus kill-and-resume: SIGINT during exploration → rerun logs "Resuming Nautilus" and completes (SIGINT after the first full update is swallowed on main too)
• A pre-A3 folder written by main (Emcee HDF, Dynesty dill, NUTS pickle, Drawer) lists in the aggregator and reloads
• CI green on unittest 3.12 / 3.13 / nojax, docs, generated-search-docs

Full API Changes (for automation & release notes)

Removed

• none (A2's provisional RawSamples/samples_from_raw in search/fit_context.py are re-exported from the adapter)

Added

• see the API Changes section above (adapter, checkpoint module, NonLinearSearch hooks, checkpointer capability, paths.stores_search_internal)
• docs/design/checkpointing.md

Migration

• Before: a search overrides samples_via_internal_from(model, search_internal) → After: implement raw_samples_from(model, internal) -> RawSamples; the base converts once
• Before: conf.instance["output"]["search_internal"] = True set by constructing Emcee/NUTS/SMC → After: never; those searches retain their archive via checkpointer.retain_after_completion
• Before: Dynesty reloads from savestate.save → After: from the dill archive once complete; savestate only resumes an unfinished run

Validation checklist (--auto run — plan was not pre-approved)

• Effective level: safe (header: safe, cap: refactor → safe)
• Plan: on the issue (refactor: samples adapter and Checkpointer/resume split (search-extensibility A3) #1677), written at start, unmodified since
• Gate: tests 3531 pass / 1 skip / 4 xfail (5 strict xfails flipped as named) + nojax 1253 · smoke afT ×7 exit 0 + Nautilus kill-and-resume + pre-A3 aggregator load · review CLEAN (Fable session over the Opus-written and Opus-integrated branch; witness basis-cited: conf.instance unchanged re-run, goldens/conformance re-run, xfail table checked) · Heart STALE release validation incomplete: no rehearsal for current source
• Human: plan sound in hindsight?
• Human: diff matches plan (no scope creep)? Note the two Dynesty xfail flips land in the Checkpointer commit, not the conf.instance commit
• Human: merge after refactor: Fitness.objective factory, PoolFactory + JAX fork rule, start_points and the run(ctx) bridge (search-extensibility A2) #1679, then log the outcome

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