Sixty-seven recordings through the whole loop

docs/handoffs/2026-09-09-the-full-cohort-through-the-loop.md

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+# The full senktide and TTX cohorts through the loop — the pointer
+
+> **Written straight into this directory on 2026-09-09 — nothing in it is half-done.** The
+> run is complete and its artifacts are in the darkroom. It was never a root signal.
+>
+> **This file carries no number derived from the recordings** (FOUNDATIONS §5: anything
+> derived from real data stays machine-local). Every measured result, every figure and the
+> full run record are in `<darkroom>/bugarach/2026-09-09-full-cohort-senktide-ttx/`;
+> resolve `<darkroom>` with `bugarach.paths.darkroom()`, or `python -m bugarach.paths`.
+>
+> **Not murderboarded**, and neither is the run record it points at — both are working
+> material for sessions in this tree, the same standing as `docs/pipeline.md`. The one
+> artifact addressed to another team, `for_fireflies/README.md`, is **marked as a draft and
+> must not be sent** until it has been through `/murderboard` and Tony has released it.
+
+Successor to [the APV+CNQX+GZ pilot](2026-09-07-the-pilot-cohort-through-the-loop.md),
+whose MAHICE and slow-bench caveats are **not** superseded by this run.
+
+## What is different from the pilot, and it is most of what mattered
+
+Both of `pipeline.md`'s blockers closed on 2026-09-08 (#507, #508, #509), and this is the
+first run to spend them:
+
+| the pilot could not | this run did |
+|---|---|
+| apply tuned settings from the command line — the six ran at shipped operating points | detected at a calibration derived from this cohort's own simulated data |
+| run a trained model on real data — nothing persisted a model | ran all six learned models from checkpoints, in a separate process from training |
+| fit background heterogeneity — six baselines were too few | fitted it from the folder; **burstiness is now the last inherited generator quantity** |
+| scan for field-step artifacts — the folder was UNCHECKED | read the producer's artifact-excluded export |
+
+## What the run found before it started
+
+**The producer's newest export had been on disk for six days and no file in this repo named
+it.** Its own README says *"for any new analysis, use this folder."* Landed as **#511**,
+which declares it as three roles beside `default` rather than instead of it — moving
+`default` re-points every existing analysis and every parity fixture, and that is a
+decision, not a housekeeping edit.
+
+That PR also carries the three things this run needed and did not have: a **floor under a
+percentage K**, a `derive_spec` path that **aggregates across recordings at each one's own
+resolved K** instead of selecting one column of the scan, and **group facets** on the
+before/after figure. Two silent defects turned up in existing code on the way — a
+hardcoded clip width that dropped the rightmost facet of any wide page, and a
+positional-tuple read across a module boundary.
+
+## Still open, in the order I would take it
+
+1. **MAHICE has still never been run on an approved folder.** Skipped here on instruction,
+   as in the pilot. Everything downstream inherits `RESET.md` §1 — a coordination number
+   nobody looked at is not a result. Expert attention, not compute.
+2. **An edge-of-grid threshold refuses on the coded branch and only warns on the learned
+   one**, and it decided what the best learned model shipped at here.
+   [The todo](../todo/2026-09-09-an-edge-of-grid-threshold-refuses-on-one-branch-and-warns-on-the-other.md)
+   names the one measurement that settles it.
+3. **Six folds cannot support a corrected pairwise winner** — that is arithmetic, not a
+   property of the detectors, and the threshold is eight. Relevant to
+   [`performance_table.md`](../performance_table.md) §1, whose replacement argument is still
+   unwritten.
+4. **Burstiness is still inherited.** `pipeline.md` says fit it from the user's own
+   baseline; rate heterogeneity now is, and this one is not.
+5. **No slow bench.** Every operating point is fast-derived and applied to a stream whose
+   measured coactivity is several times higher. Unchanged from the pilot.
+
+## Traps this run hit
+
+- **zsh does not word-split an unquoted parameter.** Building `--model a --model b` into a
+  shell variable and passing it unquoted sends **one** argument; argparse reports every
+  flag as unrecognised and the leading empty string is the tell. Write the flags out.
+- **A recording missing from a detections file is drawn at zero**, where it cannot be told
+  from a detector that ran and found nothing. The before/after figure now counts and names
+  them on the page; it caught a `--limit` smoke run immediately.
+- **A wide page loses its right-hand column silently.** Fixed in the shared renderer, but
+  the lesson generalises: the clip was a pixel constant copied from the viewport it was
+  meant to track.

docs/todo/2026-09-09-an-edge-of-grid-threshold-refuses-on-one-branch-and-warns-on-the-other.md

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+---
+status: open
+filed: 2026-09-09
+---
+
+# An optimum at the edge of its grid refuses on the coded branch and only warns on the learned one
+
+> **Not murderboarded** — working material for sessions in this tree. **If any of it
+> reaches an outside reader, murderboard that artifact first.**
+
+Found while running the full senktide + TTX cohorts through the loop, where it decided
+what the best-performing learned model shipped at.
+
+## The same condition, two verdicts
+
+This project has a written position on an optimum that lands on the boundary of the
+grid it was searched over. `bench.EdgeOfRange`'s own docstring states it:
+
+> *"Not a warning. An optimum at the edge is not an optimum — it is the search telling
+> you it stopped too early, and reporting it as a calibrated point is how a boundary
+> value once got published upstream as one."*
+
+`pick_operating_point` raises it, `tools/refit.py` reports it as an outcome, and
+`tools/settings_from_bakeoff.py` will not emit such a value without `--allow-edge`,
+which stamps the file to say so. That is the coded branch.
+
+On the learned branch the same condition is a `RuntimeWarning` from
+`learn/train.py`, the fit continues, the checkpoint is written, and the model runs on
+real recordings. `learned_settings.csv` does record `threshold_at_grid_edge`, which is
+the honest half — the value is knowable. Nothing acts on it.
+
+## What it cost here, concretely
+
+On this cohort's own generator spec, `tube` is the best learned model and second overall
+on the bake-off (F1 0.678, fold range 0.665–0.716). Its fitted threshold is **0.9999,
+the top of the searched grid `[0.0001, 0.9999]`**, flagged `threshold_at_grid_edge: yes`.
+It was saved to a checkpoint and run on all 67 recordings.
+
+So the best learned detector in this run is deployed at a threshold the coded branch
+would have refused to publish, and the refusal that exists to catch exactly this never
+fired because it is not wired to this branch.
+
+`trace` and `tiny` are at the other edge (0.0001) and also flagged, but that is their
+known degenerate-control behaviour rather than a search that stopped early — 78 calls
+across 29 recordings, one span per analysis window. Two different problems wearing one
+flag, which is its own reason to want a verdict rather than a boolean.
+
+## Why this is a decision and not a patch
+
+Making the learned branch refuse is a one-line change and it is **not obviously right**:
+
+- The threshold grid is a probability in `(0, 1)`, so "widen it" means going to
+  `1 - 1e-5` and further, and there is always another decimal place. The coded knobs have
+  natural ranges; this one does not, so an edge here may mean *"the model separates
+  cleanly and any high threshold works"* rather than *"the search stopped too early"*.
+  Those two want opposite responses.
+- `tube` at 0.9999 has a **probe rate of 1.37/min**, inside its own three-run history
+  (0.75 pilot, 2.05 published). It is not behaving like a detector at a runaway operating
+  point, which is what an edge-of-grid value would normally predict.
+- A refusal would have blocked this run's learned half entirely, and the learned half is
+  what `#508`/`#509` existed to make reachable.
+
+So the question is not "should it refuse" but **which of the two meanings an edge has
+for a probability threshold**, and that is answerable by measurement: sweep `tube`'s
+threshold past 0.9999 on the bench and see whether F1 is flat (separates cleanly) or
+still climbing (stopped too early). Nobody has.
+
+## What to do
+
+1. **Measure it.** Extend the threshold grid for the tube variants past 0.9999 and
+   report whether F1 is flat or climbing there. One probe, and it settles the question.
+2. **Then decide the verdict**, and make it the same kind of object on both branches —
+   a refusal, or a stamped-and-allowed value like `--allow-edge`, not a warning nothing
+   reads.
+3. **Separate the two flags.** `threshold_at_grid_edge` currently means both "search
+   stopped early" and "this control is degenerate". Those need different names.
+
+Related: [`2026-09-08-the-ratio-tube-cannot-count-cells.md`](2026-09-08-the-ratio-tube-cannot-count-cells.md)
+— the ratio arms read 0.00/min on the probe by arithmetic rather than by merit, which is
+the other place a learned model's number means less than it looks like it means.