prompt: record PyAutoLens#700 merged for positions-lh-penalty-accumulation

active.md

@@ -13,25 +13,6 @@
   `research/mge-lane-death` branch was never created.
   This is the canonical copy of the 2026-08-17 human-approved inference programme.
 
-## positions-lh-penalty-accumulation
-- issue: https://github.com/PyAutoLabs/PyAutoLens/issues/699
-- status: pr-open (https://github.com/PyAutoLabs/PyAutoLens/pull/700)
-- worktree: ~/Code/PyAutoLabs-wt/positions-lh-penalty-accumulation
-- repos:
-  - PyAutoLens: feature/positions-lh-penalty-accumulation
-- prompt: active/positions_lh_penalty_accumulation_bug.md
-- CONFLICT OVERRIDE (deliberate, 2026-08-17): `worktree_check_conflict` exits 1 — PyAutoLens is
-  also claimed by `version-stamp-sync-guards`. FILE-DISJOINT verified: that branch's only commit
-  (`be4c4c8b6`) touches `autolens/__init__.py` + `release.sh`; this task touches
-  `autolens/analysis/analysis/lens.py` + `test_autolens/`. Human-directed session ("get prs and
-  whatnot up", 2026-08-17). If that task starts touching `analysis/`, stop and re-coordinate.
-- summary: `log_likelihood_penalty_from` (`lens.py:163-181`) overwrites its accumulator then adds
-  the variable to itself → analysis subtracts 2x the LAST PositionsLH penalty and discards earlier
-  entries. Fix accumulation to a true sum, repin the 2 tests that encode the bug
-  (`test_analysis_imaging.py:101,:126` assert the same value for 1 and 2 penalties), add a
-  sum-of-penalties regression test, align docstring (keep 0.0-array return, not None).
-  CP-1 of the inference programme (plan §2.1); blocks all PositionsLH benchmarking.
-
 ## stored-sample-reconstruction-guard
 - issue: https://github.com/PyAutoLabs/PyAutoFit/issues/1486
 - status: library-dev — WORKSPACE HALF SHIPPED; the PyAutoFit hardening (#1486) is what remains

complete/2026/08/positions-lh-penalty-accumulation.md

@@ -0,0 +1,120 @@
+- issue: https://github.com/PyAutoLabs/PyAutoLens/issues/699 (CLOSED completed)
+- pr: https://github.com/PyAutoLabs/PyAutoLens/pull/700 — MERGED 2026-08-17 as `5d55825`, 3 files, +28/-8
+- classification: library (PyAutoLens) — bug, severity high; CP-1 of the inference programme (autolens_profiling#134, PROGRAMME.md §2.1)
+- branch: `feature/positions-lh-penalty-accumulation`
+- worktree: `~/Code/PyAutoLabs-wt/positions-lh-penalty-accumulation` — **release pending** (merge happened from a remote session; free the worktree in the next laptop session or let repo_cleanup flag it)
+
+## What was wrong
+
+`AnalysisLens.log_likelihood_penalty_from` (`autolens/analysis/analysis/lens.py:163-181`)
+overwrote its accumulator with each entry's penalty and then added the variable
+to itself, so the analysis subtracted **2x the LAST** `PositionsLH` penalty and
+silently discarded every earlier entry in `positions_likelihood_list`. With one
+entry (every SLaM stage) that is 2x the documented
+`1e8 * (max_separation - threshold)` fence; with N entries
+(double-source-plane / multi-plane) all but the last were lost. Blocked the
+entire PositionsLH benchmarking arc — every positions experiment would have
+measured an undocumented target.
+
+## Fix
+
+Accumulation is now a true sum (`x = x + y`, trivially `xp`-safe under `jnp`);
+docstring aligned to the actual 0.0-array (not `None`) no-penalty return, kept
+for the JAX path. Tests that PINNED the bug repinned: imaging single-penalty
+`-44097289521.73` → `-22048644768.18` (exactly half — the 2x), double-plane
+`-44097289521.73` → `-44140499627.75` (the true sum, now distinct from the
+single-penalty value), interferometer `-44097289569.2` → `-22048644815.85`.
+New regression assertions: analysis penalty == sum of each entry's own
+`log_likelihood_penalty_from`, the two per-plane penalties genuinely differ,
+single-entry == the entry's value exactly (no 2x). Full suite 538/538; PR CI
+green (unittest 3.12/3.13 + docs-build).
+
+## Science impact (release-notes item)
+
+Inside the threshold the penalty is exactly 0 either way — converged posteriors
+and positions-free results unchanged. Outside it the fence slope **halves**
+from the undocumented 2e8/arcsec to the documented 1e8/arcsec, so likelihood
+values in penalized regions shift. Multi-plane penalty stacking is corrected —
+previously only the last plane counted.
+
+## Traps and findings
+
+- **THE TESTS ENCODED THE BUG, AND ITS SIGNATURE HID THE DISCARD.** The
+  double-plane test asserted the SAME value for one and for two penalties —
+  under 2x-last, adding a second penalty changes nothing the tolerance could
+  see. The corrected two-plane value shows the per-plane penalties genuinely
+  differ; the regression test now pins the sum explicitly.
+- **CONFLICT OVERRIDE precedent used:** PyAutoLens was co-claimed by
+  `version-stamp-sync-guards`; `worktree_check_conflict` exits 1. FILE-DISJOINT
+  verified (that branch touches only `autolens/__init__.py` + `release.sh`) and
+  a deliberate, human-directed override was recorded in active.md rather than
+  blocking.
+- **Sizing-proxy miss:** the Brain Bug Agent scored this large(7)/split via the
+  prose-length proxy; correctly overridden to small/single-PR — the fix was one
+  accumulation line + docstring + test repins. Detailed prompts overcount.
+- **Registry-edit trap (same session):** a blanket `sed` status edit briefly
+  clobbered the stored-sample task's status line in active.md — caught and
+  restored immediately. Scope registry edits to the task's own `##` section.
+
+## Original prompt
+
+# PositionsLH penalty accumulation returns 2x the LAST penalty, discarding the rest
+
+- Work type: bug
+- Target: PyAutoLens
+- Sized: small
+- Origin: inference-programme planning pass 2026-08-17 (plan §2.1, CP-1); human: "thats
+  worrying if theres a bug in soemthing so important so defo check".
+
+## Original request (verbatim, from the programme plan critical path)
+
+> CP-1 · PositionsLH defect verify + fix (hours, laptop). Unblocks the entire positions
+> arc; every later positions result depends on it.
+
+## The bug (VERIFIED against main by direct read, 2026-08-17)
+
+`AnalysisLens.log_likelihood_penalty_from` (`autolens/analysis/analysis/lens.py:163-181`):
+
+```python
+log_likelihood_penalty = self._xp.array(0.0)
+if self.positions_likelihood_list is not None:
+    for positions_likelihood in self.positions_likelihood_list:
+        if positions_likelihood is not None:
+            log_likelihood_penalty = (          # <-- OVERWRITES the accumulator
+                positions_likelihood.log_likelihood_penalty_from(...)
+            )
+            log_likelihood_penalty += log_likelihood_penalty   # <-- doubles itself
+    return log_likelihood_penalty
+```
+
+- One penalty in the list (the common case, incl. every SLaM stage): returns **2x** the
+  documented `1e8 * (max_separation - threshold)` penalty.
+- N penalties (double-source-plane / multi-plane usage): returns 2x the **last** entry
+  only; all earlier penalties silently discarded.
+- Docstring also promises `None` when there is no penalty but the code returns a 0.0
+  array (the JAX-safe behaviour) — align the docstring, keep the behaviour.
+
+Existing tests PIN the bug: `test_autolens/imaging/model/test_analysis_imaging.py:101`
+and `:126` assert the SAME value (-44097289521.734665) for one and for two penalty
+objects — exactly the 2x-last signature. Both expected values need recomputing after
+the fix (single: base - p; two-plane: base - (p0 + p1)).
+
+## Fix
+
+Accumulate: `log_likelihood_penalty = log_likelihood_penalty + penalty_i` (JAX-traceable,
+no in-place mutation semantics needed). Update the two pinned test values, add a
+regression test asserting (a) two penalties = sum of the two individual penalties,
+(b) one penalty = exactly the `PositionsLH.log_likelihood_penalty_from` value (no 2x).
+
+## Science impact (record in PR)
+
+Inside threshold the penalty is exactly 0 either way — converged posteriors and all
+positions-free results unchanged. Outside threshold the fence slope halves (2e8 -> 1e8
+per arcsec): early-search likelihood values in penalized regions change, and
+multi-plane penalty stacking is corrected. Classify as bug-fix restoring documented
+behaviour; note in release notes that penalized-region likelihood values shift.
+
+## Do-not
+
+- Do not change the penalty formula, threshold semantics, or `PositionsLH` itself.
+- Do not return `None` (JAX path needs the 0.0 array); fix the docstring instead.

complete/index.md

@@ -6,7 +6,7 @@ Token-light navigation over the finished-work records (schema:
 only then grep a dated bucket. Curators: edit the band between the CURATED
 markers; everything below GENERATED is rebuilt.
 
-1004 records across 7 buckets.
+1005 records across 7 buckets.
 
 <!-- CURATED:START -->
 ## Highlights
@@ -94,6 +94,7 @@ _(curate hard-won records here — survives regeneration.)_
 - [point-source-light](2026/08/point-source-light.md) — Added standard and linear point-source light profiles with total-flux normalization and oversampled PSF convol…
 - [pointmass-smbh-jax](2026/08/pointmass-smbh-jax.md) — `al.mp.PointMass` and `al.mp.SMBH` failed every JAX-mode fit (user report on 2026.8.4.1). Two independent bugs…
 - [pointmass-smbh-jax-ci](2026/08/pointmass-smbh-jax-ci.md) — CI JAX coverage for the PointMass/SMBH regression class (follow-up to PyAutoGalaxy#553/#554). `misc/profiles_j…
+- [positions-lh-penalty-accumulation](2026/08/positions-lh-penalty-accumulation.md) — CLOSED completed
 - [positive-solver-divergence-diagnosis](2026/08/positive-solver-divergence-diagnosis.md) — Proved NumPy FNNLS and JAX PDIP agree to 1.715e-9 on identical systems (2.468e-13 tightened). The 8.989e-3 nat…
 - [potential-correction-env-declaration](2026/08/potential-correction-env-declaration.md)
 - [potential-correction-validation](2026/08/potential-correction-validation.md)

dashboard.md

@@ -8,7 +8,7 @@ Tasks only — the organism's health lives with the Heart (`/health`), not here.
 
 | Where | Count |
 |-------|------:|
-| [In flight](#in-flight) (`active/`) | 5 |
+| [In flight](#in-flight) (`active/`) | 4 |
 | [Parked](#parked) (`parked.md`) | 1 |
 | [Planned](#planned) (`planned.md`) | 7 |
 | [Backlog](#backlog) (`draft/`) | 139 |
@@ -49,7 +49,6 @@ Live on GitHub: [open issues](https://github.com/search?q=org%3APyAutoLabs+is%3A
 Issued — each has an open GitHub issue and usually a branch. The full record for each is in [`active.md`](active.md).
 
 - [Commit the inference-methods programme plan + knowledge ledger into autolens_profiling](active/inference_programme_ledger.md) — [issue #134](https://github.com/PyAutoLabs/autolens_profiling/issues/134) — pr-open (https://github.com/PyAutoLabs/autolens_profiling/pull/135)
-- [PositionsLH penalty accumulation returns 2x the LAST penalty, discarding the](active/positions_lh_penalty_accumulation_bug.md) — [issue #699](https://github.com/PyAutoLabs/PyAutoLens/issues/699) — pr-open (https://github.com/PyAutoLabs/PyAutoLens/pull/700)
 - [PyAutoReduce validation: slacs1430+4105 ACS reduction vs trusted legacy dataset](active/pyautoreduce_slacs1430_acs_comparison.md)
 - [Reconstructing a stored sample raises through `ignore_assertions=True`](active/to_instance_guard_gap.md) — [issue #1486](https://github.com/PyAutoLabs/PyAutoFit/issues/1486) — library-dev — WORKSPACE HALF SHIPPED; the PyAutoFit hardening (#1486) is what remains
 - [Version-stamp sync to 2026.8.17.1 + release-sed guards](active/version_stamp_sync_and_release_sed_guards.md) — [issue #235](https://github.com/PyAutoLabs/PyAutoHands/issues/235) — pr-open (https://github.com/PyAutoLabs/PyAutoLens/pull/700)