syncytium2 · syncytium2 · Aug 28, 2026 · Aug 28, 2026
diff --git a/docs/handoffs/2026-08-28-locust-is-not-cicada-and-four-things-i-got-wrong.md b/docs/handoffs/2026-08-28-locust-is-not-cicada-and-four-things-i-got-wrong.md
@@ -0,0 +1,176 @@
+# Locust is not CICADA, and four things this session got wrong on the way there
+
+**Written straight into this directory** — nothing here is half-done, so it was never a
+root signal. `HANDOFF.md` at the root belongs to the 2026-08-27 session and is still
+honest: its five PRs (#304, #292, #270, #53, #50) are all open. **Do not replace it.**
+
+Everything below is merged on `main` except **PR #364** (deploy notes 2), which was green
+and merging when this was written.
+
+---
+
+## The finding, if you read one thing
+
+**Locust is a modified port of a port, validated only at its last link, and the public page
+said it *is* CICADA's method.**
+
+```
+Cossart CICADA  ──── never validated ────▶  interface2 generate_sce_cicada  ──1e-9──▶  locust
+   (their code, MIT, 2019)                   (PARKED in f55643bf for
+    "faithful" is an assertion                over-detecting on our
+     in both repos, tested nowhere)           long SLOW transients)
+```
+
+`tools/matlab_ref/gen_ref_cicada.m` builds the parity fixture by running **interface2's
+own `generate_sce_cicada`**, so the 1e-9 result validates bugarach against interface2 and
+says nothing about CICADA. Both repos assert "faithful port"; neither contains any
+comparison against the Cossart source (grepped both).
+
+It is also a **documented partial port** — `generate_sce_cicada.m`: *"we already have
+events, so their per-cell transient-detection step is skipped."*
+
+**Established this session, so nobody re-derives it:**
+
+- **It was ported from their CODE, not the paper.** `sce_stats_utils.py` exists at the
+  cited path in `gitlab.com/cossartlab/cicada` and defines both named functions —
+  `get_sce_threshold(rasterdur, …)` and `detect_sce(traces, raster, …)`. The first
+  parameter, `rasterdur`, independently confirms the duration model the port replaces.
+- **The citation is correct.** Zenodo `10.5281/zenodo.10041434` = CICADA v1.0.3, five named
+  authors, 20 July 2020, CC-BY-4.0. Checked deliberately because the lit shelf holds
+  `denis_2020_deepcinac.pdf` — a different tool, same five authors, same year. No conflation.
+- **The lit shelf has no CICADA paper.** Only DeepCINAC. Every claim about what CICADA does
+  is sourced from its code and interface2's notes. Fetching Dard et al. (STAR Protocols)
+  would close this.
+- **The duration diagnosis has been written down since July.** interface2's
+  `docs/coordination_detectors_methods.md` §3, "Provenance (important)", names two changes
+  *"beyond tuning"* and says the original *"over-detects catastrophically on our long SLOW
+  transients (median ~4.6 s of duration-overlap swamps onset-synchrony)."*
+
+`#360` fixed the front page. **Two other sessions found more instances within the hour** —
+#363 (a handoff) and #365 (the bake-off page) — so assume there are surfaces still saying it.
+
+## ⚠ The live page is still wrong, and that is a decision waiting
+
+`bugarach.tonydefazio.com` **right now** says *"The lane marked locust **is** CICADA's
+method"* and, four sentences later, *"No method from the literature has yet been run on
+this project's recordings."* Both bold; they cannot both hold. Verified by fetching the
+page, not from git.
+
+`ed5e02e` fixes it and is **queued behind the deploy hold**. `DEPLOY_HOLD.md`'s own text
+says an actively misleading page is a reason to lift deliberately rather than route around.
+**Raised in [deploy notes 2](2026-08-28-deploy-notes-2.md), not acted on.** Tony's call.
+⚠ That note is **PR #364**, still open when this was written — if the link 404s it has not
+landed, and the decision above is then recorded only here.
+
+## What I got wrong, because the pattern matters more than the fixes
+
+Four corrections in one session, all the same shape — **a claim that was true of one
+context asserted about another**:
+
+1. **Filed a todo saying `cicada_detect` anchors on "the wrong landmark" and proposed a
+   bench run at `onset_field="peak"`.** Wrong, and acting on it would have moved the
+   detector onto the peak — the direction the project deliberately came *from*. Retracted
+   the same day in #354. The truth is **fields vs values**: `locs` is a legacy `findpeaks`
+   name holding the peak time in the store and `t50rise` in the coordination data. Tony:
+   *"pretty quickly we put t50rise into the coordination data field locs. hence the crisis."*
+2. **Compared their active-stamp duration against our full transient** and reported a
+   hundredfold gap that did not exist. The rise-interval substitution had already closed it.
+3. **Called the Cossart raster "the authors' own inference (CICADA / DeepCINAC)"** — a guess
+   about a third party's pipeline. Corrected to say only that it arrived binarised.
+4. **Reported test counts from the wrong source tree** (see the hazard below).
+
+**The one real defect that survived all that**: `rise_durations()` computes `locs -
+t50rise`, which is the rise interval on a store and **identically zero on a folder**.
+Verified: 2215 events, min 0.0, max 0.0. Latent, not live —
+`OPERATING_POINTS["cicada"]` uses fixed `active_duration_sec=1.0`. Filed as
+[`…locs-is-a-field-name-and-rise-durations-is-zero.md`](../todo/2026-08-28-locs-is-a-field-name-and-rise-durations-is-zero.md).
+
+## ⚠ Hazard that will bite the next session
+
+**A worktree's `pytest` imports the PRIMARY checkout's `src`.** One editable install in
+`.venv`, and the two are rarely at the same commit.
+
+```bash
+PYTHONPATH="$PWD/src" .venv/bin/python -m pytest tests/ -q    # correct
+.venv/bin/python -m pytest tests/ -q                          # tests another branch's code
+```
+
+It already corrupted two reported numbers: *"1454 passed, 16 skipped"* went into two PR
+messages measured against the primary tree; the true figure was **1498 passed, 3 skipped,
+1 xfailed**. **It fails toward green** — a worktree editing `src/` can pass a suite that
+never ran its change. Filed with three ranked fixes at
+[`…a-worktree-pytest-run-tests-the-primary-checkouts-src.md`](../todo/2026-08-28-a-worktree-pytest-run-tests-the-primary-checkouts-src.md);
+**Tony asked for the fix proposal next and it is not started.**
+
+Second, smaller: **`merge_when_green` correctly refuses a PR with no checks reported**, and
+GitHub sometimes creates no workflow run for a push. Re-push; it appears. Not a path
+filter — there is none.
+
+## bugarach now reads another lab
+
+`tools/import_dandi.py` (#353) turns the Cossart lab's DANDI:000219 into an export folder:
+**59 recordings, 935,965 events, 1,303 zero-event ROIs kept as `NA` rows.** `bugarach
+check` passes on all 59, `assess` runs end to end, and `build_viewer` holds their corpus
+beside ours.
+
+Written to **`<data>/exports/external/dandi_000219/`** — deliberately *not*
+`exports/bugarach/`, which `dataset.resolve()` searches for bare names. **Pass it by path;
+it is not in `current_export.toml`.**
+
+Their data is binarised, so `time_sec` is a rising edge, not a `t50rise`, and there is no
+`peak_sec` or `amp`. `PROVENANCE.md` in the folder states the cost: rates, counts and
+rankings are safe; cross-lab coincidence-within-tolerance is not available from these files.
+
+**This was the first time the project read a recording it did not produce**, which is what
+made the contract's "any producer" claim testable at all.
+
+## Data rules Tony gave this session — follow these, do not re-derive
+
+> *"Stop — don't read the .mat event store. The export folder is the input."*
+
+```python
+from bugarach import dataset
+folder = dataset.current()          # 2026-08-18_revised_2v_periods, 84 recordings
+folder = dataset.current('pensub')  # 2026-08-20_pensub_revised_2v, the same 84
+```
+
+- **Width is already in the data.** `fast width_sec = halfprom_width_findpeaks_w` (real
+  transient width, median 0.90 s); `slow width_sec = rise_interval_peak_minus_t50rise`
+  (= `peak_sec - time_sec`, median 2.00 s, max 5.5 s). **Read `width_def`, never the column
+  name.**
+- **Fast only, for now.** Tony: *"fast is closer to classical calcium events… stick with
+  fast."* There is **no declared default stream in code** — whether there should be is
+  question 2 below.
+- **Ask when there are options; do not analyse all of them.** And *"if you cannot find the
+  specific data associated with this project, FULL STOP."* Both are standing instructions,
+  earned the hard way — the case report is in `syncytium2/short-course`.
+
+## Open decisions, all Tony's
+
+1. **Lift the hold for `ed5e02e`?** The live page is misattributing a result to another lab.
+2. **Should "fast" become a declared default stream?** FOUNDATIONS §3 declines to privilege
+   one *on purpose* (streams are generic; most labs have one), so declaring a default
+   contradicts a deliberate design decision. Filed nowhere — it is in the `SESSIONS.md`
+   block and here.
+3. **The `conftest.py` + guard-test fix** for the worktree hazard. Tony: *"then we can
+   continue with your fix proposal."* Not started.
+4. **`syncytium2/short-course` audience call** — the case report recommends itself for the
+   beginner course and competes with the sibling case for one slot.
+
+## Filed this session, all open
+
+| file | what it is |
+|---|---|
+| [`docs/todo/…locs-is-a-field-name…`](../todo/2026-08-28-locs-is-a-field-name-and-rise-durations-is-zero.md) | `rise_durations()` is zero on folder input; latent, not live |
+| [`docs/todo/…worktree-pytest…`](../todo/2026-08-28-a-worktree-pytest-run-tests-the-primary-checkouts-src.md) | the hazard above, three ranked fixes |
+| [`docs/sapper_feedback/…sap007…`](../sapper_feedback/2026-08-28-sap007-cannot-tell-an-importer-from-an-analysis.md) | SAP007 cannot tell an importer from an analysis; also, its exclusion list is now half backlog and half permanent, so its length measures nothing |
+
+## Provenance
+
+Written 2026-08-28 by the session that made #353, #354, #360 and #364, at Tony's request
+when nearing compaction. Landed also: `syncytium2/short-course` `42e981c`, a case report on
+this session's own data-fabrication failure. Every number here was re-derived at writing
+time; the live-page quotes were fetched over HTTP. **Review scope: a single-pass claim
+check (role 1) against git, the files and the live page — not an eleven-role murderboard**,
+stated because a handoff claiming more review than it had is the defect this repo files
+incidents about.
diff --git a/docs/handoffs/README.md b/docs/handoffs/README.md
@@ -78,3 +78,4 @@ The rule was missing a third option. This is it.
 | [the guards that could not fail](2026-08-27-the-guards-that-could-not-fail.md) | 2026-08-27 | four checks that reported success while looking at nothing: a size canary printed where a spill discards it, a board gate matching by substring, a liveness test that skipped in the only place it promised to shout, and the census built to fix the first — which measured nothing on Linux and said all checks pass. Closes items 1–3 of the hook audit, and explains what *"send it upstream"* actually costs. **Written straight into this directory**: it was never a root signal, because nothing in it was half-done |
 | [what #351 changes under the deploy](2026-08-28-what-351-changes-under-the-deploy.md) | 2026-08-28 | for whoever lifts the [deploy hold](../DEPLOY_HOLD.md). `53b1d62` is not a content change: it swaps how all seventeen long loops schedule themselves — only four in the sweep — adds the page's first `beforeunload` prompt, and stamps fifty inputs against autofill. Carries the measured background cost that motivated the swap (a 20-setting LoCo sweep: 10 s in front, ~25 min if left in a hidden tab), the residual `⚠` that the swap's full effect **cannot** be measured under automation and needs one look at the live page, two traps that bite any deploy session regardless, and a retraction of a wrong test count already merged into PR #351's message. **Written straight into this directory** — nothing in it is half-done |
 | [deploy notes 2 — the live page is wrong about another lab](2026-08-28-deploy-notes-2.md) | 2026-08-28 | **the companion to the row above**, covering the other queued commits. The public page tells readers `locust` **is** CICADA's method and, four sentences later, that no method from the literature has been run here; both are bold and they cannot both hold. The fix `ed5e02e` is queued behind the deploy hold, whose own text says an actively misleading page is a reason to lift deliberately rather than route around — raised for a person, not acted on. Also: **three sessions have edited `raster_viewer.html` since the last deploy** and nobody has driven the combination |
+| [locust is not CICADA, and four things this session got wrong](2026-08-28-locust-is-not-cicada-and-four-things-i-got-wrong.md) | 2026-08-28 | the derivation chain is validated only at its last link — `gen_ref_cicada.m` builds the 1e-9 fixture from interface2's own port, so nothing compares anything to the Cossart source, and interface2 **parked** that port for over-detecting. Established that it came from their **code** (`sce_stats_utils.py`, both functions verified) and that the citation is correct. Carries the live page still saying `locust` **is** CICADA's method, four self-corrections in one session with the pattern they share, the data rules Tony gave, and the hazard that **a worktree's `pytest` imports the primary checkout's `src`** — which had already put two wrong test counts into PR messages |