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1 change: 0 additions & 1 deletion active.md
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- epic: autonomous-orchestrators (pilot 4c follow-up)
- tier: glance — merge mode: auto-merge on green if the Witness passes, post-merge summary (non-PASS Witness → human /prm)


## autonomous-orchestrators-p4c
- issue: https://github.com/PyAutoLabs/PyAutoBrain/issues/574
- issued: 2026-11-04
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### C. Bookkeeping, tests and corrections

10. **`gradient.json` `point` mislabel.** Source: `draft/bug/autolens_profiling/gradient_json_point_label_standard_cells.md` (glance; a quick win, do it early).
10. **`gradient.json` `point` mislabel.** Source: `draft/bug/autolens_profiling/gradient_json_point_label_standard_cells.md` (glance; a quick win, do it early). **Shipped** in autolens_profiling#518 (9d2ee2d3d, 2026-11-02); draft closed 2026-11-05 as `complete/2026/11/gradient-json-point-label.md`.
11. **Correct the #515 research note.** In autolens_profiling `wiki/research/gradient_campaign_impact_border_tie.md`, the table row for `point_source_image/image_plane` and `cluster/image_plane` says *autodiff* is exactly zero. It is the **FD** that is zero and autodiff that is nonzero (mechanism E). Fix that row and link item 9.
12. **Verify the rectangular mapper row-weights bug is fixed.** Source: `draft/bug/autoarray/rectangular_mapper_bilinear_row_weights.md` (filed 2026-08-26, Status: draft). The code in `autoarray/inversion/mesh/interpolator/rectangular.py` now carries comments saying the mirrored row weights and the `ceil` bracketing were fixed (autolens_workspace_test#279). Verify, then retire it with the fixing commit.
13. **Critical-curve / caustic `jit` / `grad` parity test.** Source: `draft/test/autolens_workspace_test/jax_zero_contour.md` (notify).
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- summary: superseded by a different fix — closed. Commit 4d8290555 (2026-09-20, "fix: fall back to curl when arXiv rejects urllib with 406") keeps urllib but retries any 406 once through `curl` (already on the runner) before the back-off ladder, rather than moving `_get()` to `requests`. The 406 retry from #412 is kept, so prompt items 2–3 are covered by a dependency-free route. Item 4 (PyAutoMemory) shipped separately in PyAutoMemory#143 (record `arxiv-refs-api-errors`).
- evidence: `arxiv_papers.yml` scheduled runs 2026-10-29..11-05 all green. Of the two failures in the last 10 runs, 2026-10-27 was a pyautolabs-bot token 403 pushing to PyAutoMemory (not arXiv), and 2026-10-28 was HTTP 429 on all six attempts from the shared runner egress (rate-limiting, not the 406 fingerprint block).
- witness: the cache-busted urllib-vs-requests live probe (prompt item 1) was NOT run; this close rests on the run history above, not on a fingerprint measurement.
- follow-up candidate (not filed): on a 429 day, `--livecheck` spends a full ~6 min ladder before the fetch step spends another, doubling load on a throttled egress. Worth filing only if 429 days recur.
- found by: queue check-in 2026-11-05.

## Original prompt

# arXiv's Fastly edge refuses `urllib.request` outright — retrying a 406 only delays the failure

Type: bug
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- summary: already shipped — closed as stale draft. PyAutoMemory#143 (merged 2026-11-03, merge 1f22de7; commits 0c3e2dc, 625b583): `resolve_title()` raises `ArxivAPIError` on transport/parse failure so `None` means only "arXiv answered, no unique match"; `_api_query()` has a back-off ladder shaped like Mind's `_get()` (406/429/5xx, Retry-After capped) plus the curl-on-406 fallback; `backfill_arxiv_refs.py` gains `api_failed`/`unattempted` counters, stops at the first API failure and exits 1 (stricter than "when transport failure dominates"); `arxiv_refs.yml` writes an "arXiv API failure" step-summary banner and goes red; `--mark-unresolved` never NOTE-marks after a transport failure.
- witness: `test_witness_a_429_is_an_api_failure_not_a_non_match` in tests/test_arxiv_refs.py — fails on the pre-0c3e2dc source, passes now; Memory suite 286 passed, test_arxiv_refs.py 38 passed, `make validate` passes (2026-11-05).
- history check: 2026-09-13..20 touched reading-queue.md/arxiv-inbox.md in 575978a and b3233c6 only; neither added a NOTE line — nothing was mis-marked during the outage.
- not done: client not switched to `requests` (curl fallback makes it unnecessary).
- found by: queue check-in 2026-11-05.

## Original prompt

# `arxiv_refs.py` swallows every API error, so an arXiv outage resolves nothing and still reports green

Type: bug
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- summary: superseded/shipped — autocti_visualization#8 (2026-10-23), record `complete/2026/10/autocti-viz-render-from-mains.md`: render.yml renders from the library mains instead of waiting for a PyAutoCTI release; render 40032877406 went green and dispatched eyes-refresh (the Witness). That record's original prompt duplicates this draft.
- found by: draft-queue sweep 2026-11-05 (read-only audit against the Mind ledger + GitHub commit/PR/code search); closure approved by the human.

## Original prompt

# autocti_visualization render.yml fails on the released stack until PyAutoCTI releases

Type: bug
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- summary: already shipped, closed as a stale draft. PyAutoBrain 15317af (merged via #564, 2026-11-03) "phase 2 — the remaining GitHub legs onto the --github-data seam". The upkeep leg now reads through the seam. The versions, community and resume legs had already been retired from the board by 41ec5c5 (2026-10-08). So a remote render has zero unread legs, which meets the umbrella's headline criterion.
- witness: `test_a_remote_render_reads_all_four_phase2_legs` in Brain `tests/test_board_github_data.py`; the file gives 10 passed, 2026-11-05.
- found by: stale-draft sweep 2026-11-05. The shipping session merged without closing the draft. Closure approved by the human.

## Original prompt

# Board phase 2: the remaining four legs onto the seam

Type: feature
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60 changes: 60 additions & 0 deletions complete/2026/11/compile-drift-single-sample.md
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- summary: shipped in PyAutoBrain#588 (merge e822697, 2026-11-05), commit ed0782c. Decision: option (a), taken by the agent as decide-and-flag and accepted by the human on 2026-11-05. The 2x `COMPILE_DRIFT_RATIO` band and the 1 s floor stay as a gross flag. Each drifted row from `ingest --axis compile` now carries `comparison` (`single-sample` / `repeat-summarised`), `pinned_repeats`, `observed_repeats` and `caveat` (`SINGLE_SAMPLE_CAVEAT`: "single-sample endpoint(s): a gross 2x-band flag from one pinned timing vs one observed timing, not a measured change"). `triage --axis compile` passes these through. A row counts as repeat-summarised only when both endpoints carry `compile_repeats` >= 2 (P7's rule). Compile cost only.
- witness: `test_compile_drift_is_reported_as_a_single_sample_comparison` (synthetic: 4.0 s → 10.0 s drifts with the caveat, 4.0 s → 6.0 s does not) and `test_compile_drift_reports_repeat_counts_when_the_data_carries_them`. Brain suite 1578 passed, 1 skipped. CI pytest 3.12/3.13 green at 0f82a07.
- follow-up (not filed): no producer writes `compile_repeats` yet, so every real drift reports single-sample. autolens_profiling's `jax_compile` tooling could write it.
- also in #588: the intake `census()` epic-companion skip (dashboard 286 → 239 prompts) and the organ-target Memory-gate spelling test (record `intake-memory-line-organ-targets`).

## Original prompt

# Profiling conductor compile drift compares one point against one point

Type: bug
Target: pyautobrain
Repos:
- PyAutoBrain
Themes:
- measurement-tools
Difficulty: small
Autonomy: supervised
Priority: medium
Consequence: judge
Status: draft
Filed: 2026-10-09
Related: https://github.com/PyAutoLabs/autolens_profiling/issues/362

## Context

The timing-noise audit of autolens_profiling (`results/notes/timing_noise_audit_2026_10.md`, #362)
found that the project dashboard's release drift badge (P7) compared single-sample endpoints, and
fixed it there (#405: within-band → `insufficient` unless both endpoints carry a repeat summary;
#408: compare like estimators only). The audit note records that the Brain profiling conductor's
`COMPILE_DRIFT_RATIO` rule (`agents/conductors/profiling/_profiling.py:88`, used at ~513) shares
P7's point-vs-point limitation, and that "a separate Brain task should decide whether compile drift
follows; this audit does not edit Brain".

## Decide

Whether the conductor's compile-drift check should (a) keep its generous 2x band as a gross flag
with an explicit "single-sample" caveat, as P7's `drifted`/`improved` now do, (b) require repeats or
an interval before reporting drift, or (c) stay as is with a documented reason. Keep compile and
execution costs separate. Synthetic witness required for any change.

## Original request (chat 2026-10-09)

"prm and then do 3b and leftovers fully wrap up --auto" — filed as the Brain hand-off named in the
audit note; not part of the #362 PRs.

## Implemented 2026-11-05 — awaiting the human's call on option (a) and a PR

Decide-and-flag: the agent took **option (a)**. The change is on PyAutoBrain branch
`ccr-f98d2a4d-92r7rv`, commit ed0782c, unmerged with no PR yet. The 2x
`COMPILE_DRIFT_RATIO` band and 1 s floor stay as a gross flag. Each drifted row now
carries `comparison` (`single-sample` / `repeat-summarised`), `pinned_repeats`,
`observed_repeats` and `caveat` ("single-sample endpoint(s): a gross 2x-band flag from
one pinned timing vs one observed timing, not a measured change"), and
`triage --axis compile` passes them through. Repeat counts come from an optional
`compile_repeats` field (both sides ≥ 2, P7's rule), which no producer writes yet, so
every real drift reports single-sample today. Compile cost only.
Tests: `test_compile_drift_is_reported_as_a_single_sample_comparison`,
`test_compile_drift_reports_repeat_counts_when_the_data_carries_them`. Brain suite 1576
passed. Possible follow-up: autolens_profiling's `jax_compile` tooling writes `compile_repeats`.
Tier stays judge, so this needs a human /prm.
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- summary: parent closed. Phase 1, the presentation change, shipped in PyAutoBrain#526 (merge 92de427, 2026-10-15; record `complete/2026/10/cortex-project-readability.md`). Phase 2, output accounting, stays open as its own draft, `draft/feature/cortex/output_summary.md`, which carries the human's two-phase approval and the verbatim request reference. It still needs plan approval before any source change.
- found by: stale-draft sweep 2026-11-05. Closure approved by the human.

## Original prompt

# Human-readable Cortex Projects dashboard

Targets: @PyAutoBrain @PyAutoCortex
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- summary: superseded by the human 2026-10-30 (the draft's own banner); `complete/2026/10/sky-orientation-dr1-p1.md` records "AGREED: the old rgb-flip bug draft … is superseded". It was never moved out of draft/.
- found by: draft-queue sweep 2026-11-05 (read-only audit against the Mind ledger + GitHub commit/PR/code search); closure approved by the human.

## Original prompt

# euclid_dr1: every dataset rgb.jpg is upside down relative to the VIS FITS — flip them all, locally and on RAL

> **SUPERSEDED 2026-10-30 (human).** The flip ran on 2026-09-20 (`preprocess/flip_rgb.py`, originals kept as
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- summary: already shipped before it was filed — PyAutoFit#1538 (96dad519) + PyAutoGalaxy#589 (merge 0fbe863d, 2026-08-28), record `complete/2026/08/ell-comps-disk-constraint.md`; the draft was filed 2026-09-01 (duplicate). Unfiled residue per that record: a workspace example and a campaign re-measure.
- found by: draft-queue sweep 2026-11-05 (read-only audit against the Mind ledger + GitHub commit/PR/code search); closure approved by the human.

## Original prompt

# A joint unit-disk constraint (or reparameterisation) for `ell_comps`

Type: feature
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- summary: superseded by human decision — autolens_visualization#5 and #14, record `complete/2026/10/viz-all-dataset-types.md`: group and cluster producers shipped (dataset.png and fit.png, cluster per source plane); full figures were replaced by "bespoke via Eyes" follow-ups.
- found by: draft-queue sweep 2026-11-05 (read-only audit against the Mind ledger + GitHub commit/PR/code search); closure approved by the human.

## Original prompt

# autolens_visualization: group and cluster galleries (point-source + extended)

Type: feature
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- summary: superseded by human decision — autolens_visualization#5 (+ 465fc508 datasets), record `complete/2026/10/viz-all-dataset-types.md`: the multi_galaxy dataset, simulator and producer shipped, writing dataset.png and fit.png only (not the full all-true plots), as the human decided.
- found by: draft-queue sweep 2026-11-05 (read-only audit against the Mind ledger + GitHub commit/PR/code search); closure approved by the human.

## Original prompt

# autolens_visualization: multi-galaxy gallery — producer and dataset

Type: feature
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- summary: already shipped — closed as stale draft. Item 1 (code): commit 679b1319f (2026-10-16) made `shadow_count_line()` append "window reached" once graded rows ≥ SHADOW_TARGET; it now also cites the ruling (SHADOW_RULED). Item 2 (human doctrine call): the human ruled 2026-11-04 — `glance` granted, narrowed; rows keep accumulating, with unattended merges in a stage-2 sub-window (record `complete/2026/11/glance-tier-ruling.md`, PyAutoBrain#567, PyAutoMind#529).
- witness: `tests/test_autonomy_log_shadow.py` passes on main; autonomy_log.md count line reads "…window reached — ruled 2026-11-04: `glance` granted, narrowed…" (2026-11-05).
- found by: queue check-in 2026-11-05.

## Original prompt

# Glance shadow window reached 20/20 clean — count line must say "reached"; record the glance confirmation decision

Type: bug
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- summary: already shipped — autolens_profiling#518 (9d2ee2d3d, merged 2026-11-02 22:38, filed 16:18 the same day) records the real gradient evaluation point: 53 gradient.json records now say "iid draw 0"; the 18 still saying prior_medians are MGE cells, where that label is correct.
- found by: draft-queue sweep 2026-11-05 (read-only audit against the Mind ledger + GitHub commit/PR/code search); closure approved by the human.

## Original prompt

# Standard-size gradient cells record `"point": "prior_medians"` while evaluating at iid draw 0

Type: bug
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- summary: already shipped — euclid_strong_lens_modeling_pipeline 37034f22 (2026-09-25, default branch) "activate.sh: keep Python/JAX caches off $HOME on HPC"; code search finds `PYAUTO_HPC_CACHE` in activate.sh on main.
- not done: the fake-base witness was not re-run.
- found by: draft-queue sweep 2026-11-05 (read-only audit against the Mind ledger + GitHub commit/PR/code search); closure approved by the human.

## Original prompt

# Keep caches off `$HOME` on HPC — phase 2 remainder: euclid pipeline `activate.sh`

Type: maintenance
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- summary: already shipped — closed as stale draft. The `_with_memory` gate in `agents/conductors/intake/_intake.py` landed in PyAutoBrain 557f8e0 and ba38413: organ targets get no `Memory:` line. The organ set comes from `PyAutoMind/repos.yaml` (`_sizing.ORGANISM_REPOS` = `category: organ`, plus `_intake._ORGANS_DIR_REPOS` for repos under `organs/`, which covers PyAutoScientist). `Target:` is normalised by `_sizing.normalise_repo` (case, leading `@`, path suffix).
- witness: PyAutoBrain branch `ccr-f98d2a4d-92r7rv` commit 906b5dd adds `test_organ_target_spellings_get_no_memory_line` (organ spellings `pyautobrain`, `@PyAutoBrain`, `PYAUTOMIND`, `@PyAutoBrain/agents`, PyAutoScientist get no line; a library target still gets one); tests/test_intake_memory.py 8 passed; Brain suite 1576 passed, 1 skipped (2026-11-05). The test-only commit is unmerged and needs a PR.
- found by: queue check-in 2026-11-05.

## Original prompt

# intake classify --file injects an unrelated Memory: line on organ-targeted prompts

Type: bug
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- summary: already shipped — PyAutoLabs/autolens_jax_joss: 9c66b020 (birth, 10 benchmark scripts), 64204f69 (A100 sweep of 8 benchmarks), 6b14c207 (paired_example refs); `complete/2026/09/workspace-dead-weight-cleanup.md` already flagged it as looking shipped. The 5-minute runtime targets stay tracked in joss_cluster_benchmark_tuning.
- found by: draft-queue sweep 2026-11-05 (read-only audit against the Mind ledger + GitHub commit/PR/code search); closure approved by the human.

## Original prompt

# autolens_jax_joss benchmark repo + real-data start_here pairing

Type: feature
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- summary: decided and shipped — the human approved all 39 designations (datacube/delaunay gpu_a100 held provisional); PyAutoPulse#84 (bcaf6b86, 2026-10-31), record `complete/2026/10/likelihood-lifecycle-p3-designation-records.md` (its Witness cites Appendix B of this proposals file as approved); epic ledger updated.
- found by: draft-queue sweep 2026-11-05 (read-only audit against the Mind ledger + GitHub commit/PR/code search); closure approved by the human.

## Original prompt

# Likelihood lifecycle phase 3: designation proposals for the completed campaigns (2a imaging, 2b interferometer, 2c point source) — DRAFT for the human

Type: research
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- summary: already shipped — PyAutoFit#1556 (merged 2026-09-01) wires iterations_per_quick_update into the MultiStart gradient step loop (ba22d5ba2 flips the tripwire to assert quick updates fire); 94a658b32 makes MultiStart* honour iterations_per_quick_update / live_visual_update.
- found by: draft-queue sweep 2026-11-05 (read-only audit against the Mind ledger + GitHub commit/PR/code search); closure approved by the human.

## Original prompt

# MultiStartGradient searches ignore iterations_per_quick_update and live_visual_update while announcing the cadence…

Type: bug
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- summary: superseded — PyAutoFit 196abf39a (2026-10-08) "Analysis.is_jax as the single JAX probe": Nautilus reads `analysis.is_jax`, whose body is `bool(getattr(self, "_use_jax", False))`, and `PriorFactor(FactorKW, Analysis)` inherits it, so the unguarded `_use_jax` read that crashed EP prior-factor steps is gone.
- not done: the EP regression test the draft asked for (Nautilus as default_optimiser over a FactorGraphModel with PriorFactors, one step) was not found; re-file as a small test task if wanted.
- found by: draft-queue sweep 2026-11-05 (read-only audit against the Mind ledger + GitHub commit/PR/code search); closure approved by the human.

## Original prompt

# Nautilus as an EP default_optimiser crashes on PriorFactors (reads analysis._use_jax unguarded)

Type: bug
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- summary: already shipped — PyAutoNerves#169 (merge 8eca4b3, 2026-09-15), record `complete/2026/09/colab-bootstrap-lazy-deps.md`: `setup_colab.py` pins nautilus-sampler==1.0.5 and `TestSpecifiersTrackAutofit` reads PyAutoFit's pyproject at run time — the Witness.
- found by: draft-queue sweep 2026-11-05 (read-only audit against the Mind ledger + GitHub commit/PR/code search); closure approved by the human.

## Original prompt

# Colab pins `nautilus-sampler==1.0.4` while PyAutoFit declares `1.0.5`

Type: bug
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- summary: already shipped — PyAutoNerves#203 (issue #202, merged 2026-10-17), record `complete/2026/10/workspace-freshness-stamp.md`: floor-only workspaces no longer generate false staleness warnings; that record's original prompt is a twin of this draft.
- found by: draft-queue sweep 2026-11-05 (read-only audit against the Mind ledger + GitHub commit/PR/code search); closure approved by the human.

## Original prompt

# PyAutoNerves emits a false "workspace is stale, git pull" warning…

Type: bug
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