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fix: deep audit PR A — repair skill recipes against the installed stack#36

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Jammy2211 merged 5 commits into
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feature/assistant-deep-audit
Jul 8, 2026
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fix: deep audit PR A — repair skill recipes against the installed stack#36
Jammy2211 merged 5 commits into
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feature/assistant-deep-audit

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Part of #35 (deep audit, phase A of C — do not auto-close). Skill prose review: all 19 mature skills read end-to-end against _style.md, with every code-recipe symbol introspected against the installed 2026.7.6 stack. The review standard was "would this recipe steer a weaker model correctly?" — recipes are executed by whatever model the user runs.

What changed

  • al_custom_profile — recipe used three nonexistent APIs (Dictable mixin, _radii_from_grid, _b_n) and directed default-priors YAML into the installed PyAutoGalaxy config (source-edit-boundary violation). Rewritten around the real base-class helpers (elliptical_radii_grid_from, explicit Ciotti–Bertin b_n), workspace config/priors/, explicit no-default-priors gotcha. Corrected recipe executed against the installed stack.
  • al_run_slam_pipeline — recipe imported a slam module + slam_pipeline_main driver that have never existed; replaced with the real copy-slam_start_here.py pattern (stages are inline functions chained by af.Result), positions wiring verified.
  • al_configure_searchiterations_per_updateiterations_per_quick/full_update; UltraNest/PySwarms removed from the menu (not exposed by installed autofit).
  • al_load_resultstracer.einstein_mass_angular_from no longer exists; now routes through al.LensCalc.from_tracer (verified, cited).
  • al_inspect_source_reconstruction — invented inversion attributes replaced with verified names (reconstruction, reconstruction_dict, mapped_reconstructed_data); leads with subplot_fit_imaging.
  • al_chain_searches — phase-2 recipe used the exact Delaunay+ConstantSplit combination that open regression PyAutoArray#332 crashes on; switched to RectangularUniform+Constant with the regression noted inline; the inspection skill's warning block updated and dated.
  • al_debug_fit_failure — mixed-generation aggregator snippet (undefined names, wrong result access) replaced with the load-results-consistent tracer.json + FitImaging pattern.
  • al_prepare_imaging_data — recipe ended on a bare interactive plot call; now saves + prints dataset.png and holds for the real-data inspection.
  • al_plot_tracer — multi-plane branch referenced the retired PlanePlotter, contradicting its own flat-API preamble.
  • _style.md / AGENTS.md — plot-open offer made platform-aware (was macOS-only open); typo fix.

Verified clean (no changes needed): al_run_search, al_build_imaging_model, al_simulate_dataset, al_plot_fit_residuals, al_ingest_paper, al_setup_environment, al_update_wiki, al_refresh_api_docs; al_audit_skill_apis claims spot-checked (its tool is PR B's subject). al_build_interferometer_model got minor accuracy edits (transformer choice documented where it lives; pointless settings= dropped).

Validation

  • Symbol audit: 55 files, 116 unique symbols, 0 missing/broken.
  • make validate-literature-citations — passes.
  • Relative-link sweep over skills/ + AGENTS.md — clean.
  • Corrected custom-profile recipe run end-to-end (correct shape, finite, serialises, af.Model integration).
  • Tests/smoke: n/a — documentation repo, no test dir / script surface (stated per the ship-gate applicability rules).

Recorded for the next phases (no changes here)

  • PR B (tooling): PreToolUse gate's documented PYAUTO_SKIP_API_GATE=1 per-command bypass cannot work (hook reads its own process env, not command text); gate conflates stack-import failure with symbol staleness and repeats the full error wall per symbol; --check-version prints the mismatch wall three times; version pin 2026.5.29.4 vs installed 2026.7.6.649 (standing Heart finding — pin is release-owned).
  • PR C (wiki): wiki/core/concepts/non_linear_search.md, wiki/core/api/searches.md tables and wiki/core/index.md still recommend UltraNest/PySwarms; wiki/core edits go through al_update_wiki.

🤖 Generated with Claude Code

Jammy2211 and others added 5 commits July 8, 2026 17:03
al_custom_profile's light-profile recipe used three APIs that don't
exist in the installed stack (Dictable mixin, _radii_from_grid, _b_n)
and told users to write priors YAML into the installed PyAutoGalaxy
config, crossing the source-edit boundary. Rewritten around the real
base-class helpers (elliptical_radii_grid_from, explicit Ciotti-Bertin
b_n), no mixin, workspace config/priors/, and the no-default-priors
gotcha made explicit; the corrected recipe was executed against the
installed stack. al_prepare_imaging_data's minimal recipe ended with a
bare interactive plot call contradicting the plot-output rules; it now
saves and prints the dataset.png path and holds for the real-data
inspection. al_build_interferometer_model dropped a pointless
settings=al.Settings() and documents the transformer choice where it
actually lives (Interferometer.from_fits).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
al_configure_search: iterations_per_update no longer exists on Nautilus
(now iterations_per_quick/full_update); UltraNest and PySwarms are not
exposed by the installed autofit, so the other-searches menu now lists
what actually ships (DynestyDynamic, Zeus, BFGS/LBFGS, Drawer).
al_run_slam_pipeline: the recipe imported a slam module and
slam_pipeline_main driver that have never existed — replaced with the
real pattern grounded in slam_start_here.py (stages are inline
functions chained by af.Result; copy the template via init-slam and
adapt), with the positions-likelihood wiring verified against the
installed API.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Tracer no longer carries einstein_mass_angular_from (lensing derived
quantities moved to al.LensCalc.from_tracer/from_mass_obj) —
al_load_results now shows the LensCalc route with a source citation.
al_debug_fit_failure's residual-inspection snippet mixed aggregator
generations with undefined names; replaced with the al_load_results-
consistent tracer.json + FitImaging pattern with explicit imports and
saved (not interactive) plot output. al_plot_tracer's multi-plane
branch referenced the retired PlanePlotter, contradicting its own
flat-function-API preamble. Every symbol in both plotting skills
verified against the installed stack.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…ers hit it

al_inspect_source_reconstruction's snippet used inversion attributes
that never existed (reconstruction_dict_of_mapper,
reconstructed_data_dict); replaced with the verified 2026.7 names
(reconstruction, reconstruction_dict, mapped_reconstructed_data) and
lead with subplot_fit_imaging whose final panel is the reconstruction.
al_chain_searches' phase-2 recipe used exactly the Delaunay +
ConstantSplit combination that open regression PyAutoArray#332
crashes on, with no warning — switched to RectangularUniform +
Constant with the regression note inline; the warning block in the
inspection skill now names both broken combinations and is dated to
the current stack.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The plot-path announcement hardcoded the macOS-only 'open' command in
AGENTS.md and twice in _style.md; the offer is now platform-aware
(open / xdg-open / explorer.exe-wslview). Fixes a doubled 'the' in
_style.md's Iteration section.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
@Jammy2211 Jammy2211 marked this pull request as ready for review July 8, 2026 17:25
@Jammy2211 Jammy2211 merged commit 46cde1b into main Jul 8, 2026
1 check passed
@Jammy2211 Jammy2211 deleted the feature/assistant-deep-audit branch July 8, 2026 17:26
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