OpenFUSIONToolkit · matt-pharr · Jul 8, 2026 · Jul 8, 2026 · Jul 8, 2026
diff --git a/CLAUDE.md b/CLAUDE.md
@@ -2,117 +2,60 @@
 
 Modern GUI + standalone Python library for **3D magnetic-sensor analysis of tokamak MHD
 instabilities** — quasi-stationary (locked) modes and rapidly-rotating modes. Device-agnostic
-(DIII-D, NSTX-U, … and synthetic machines for sensor design). Built for the 2026 Magnetics
-Hackathon.
-
-## Hackathon teammates — read this first
-This is a **four-team** effort. **Before doing substantive work, ask the user who they are and
-which team they're on**, then stay in that lane so you help them effectively (and so two people's
-instances don't redo the same work):
-- **Rapid Rotators** — rotating-mode / MODESPEC analysis (+ Olena on the rotating GUI)
-- **Slow Rollers** — quasi-stationary / SLCONTOUR analysis (+ Meg on the QS GUI)
-- **Data Streamers** — DIII-D data fetch + the data layer
-- **Interfacers** — GUI shell + the GUI⇄analysis contract/seam
-
-**Don't do other teams' work.** Coordinate shared cleanup via Slack or a GitHub PR before
-starting. If you're unsure whose lane something is, ask.
-
-## Current status (Day 3, 2026-07-01)
-The full **fetch → process → service → GUI** path is live end-to-end for **both** the
-**rotating-mode (MODESPEC)** and the **quasi-stationary (SLCONTOUR)** analyses against real
-DIII-D shots:
+(DIII-D, NSTX-U, … and synthetic machines for sensor design).
+
+## Architecture — how it fits together
+The full **fetch → process → service → GUI** path runs end-to-end for **both** the
+**rotating-mode (MODESPEC)** and the **quasi-stationary (SLCONTOUR)** analyses against real shots:
 - **Fetch:** `magnetics.data.fetch.toksearch` (mdsthin via the `cybele` ssh-config alias, or a
   cluster-side `python -m` run orchestrated by `fetch/remote.py`) writes one HDF5 per shot to
   `data/datafile/` (gitignored); read back via `magnetics.data.h5source`. The GUI can trigger a
   pull from the left rail (`PullControl` → `POST /api/fetch`).
-- **Process:** `core/spectral.py` (MODESPEC) is real and pure. The **SLCONTOUR quasi-stationary
-  fit is now live end-to-end** via the reference pipeline in `magnetics._slcontour/` (xarray,
-  self-contained OMFIT shim) adapted by `core/qs_bridge` — real K / χ² / modes for shots pulled
-  with the Bp LFS midplane array. The pure `core/quasistationary` port exists but is not yet wired
-  in production (#40).
+- **Process:** `core/spectral.py` (MODESPEC) is real and pure. The SLCONTOUR quasi-stationary fit
+  runs end-to-end via the reference pipeline in `magnetics._slcontour/` (xarray, self-contained
+  OMFIT shim) adapted by `core/qs_bridge` — real K / χ² / modes for shots pulled with the Bp LFS
+  midplane array. A pure `core/quasistationary` port exists but is not yet wired in production (#40).
 - **Service:** `service/app.py` — `GET /api/node/{shot}/{node_id}` serves `kind`-nodes from
-  `service/nodes.py`; `/api/machines` lists fetched shots (mock fallback when none). The `qs_fit`
-  SSE stream is still mock.
-- **Seam (merged, PR #11):** `nodes.py` forwards GUI query params and serves the core's real
-  `mode_number` / `coherence` / `n_spectrum` nodes + a cursor-aware `phase_fit` — **the rotating
-  path is unblocked** (the GUI can consume real data + wire its knobs).
-- **QS live (Day-3 night):** `qs_fit` / `phi_t` / `fit_quality` / `chi_sq_t` / sensor-map / signal
-  nodes serve the **real** SLCONTOUR fit. Shots pulled rotating-only (no Bp LFS midplane array)
-  return a clean 422 and the QS tab shows a "no quasi-stationary array" banner. Remaining fidelity
-  gap: the data layer's per-sensor σ (the fit uses a constant σ; helicity is computed from Ip·Bt).
-- **Geometry shot-indexed (Day-3 night):** `data/device/diiid.json` sensor availability + positions
-  are now segmented back to shot 124400 (legacy dense set) / 151593 (3D-upgrade). The Sensors tab
-  renders wall + vacuum vessel + perturbation coils + saddle loops (2D honoring each loop's tilt).
-- **NSTX/NSTX-U live (branch `feature/nstxu-data-fetch`):** the fetch is **device-generic** — a
-  device with `access:"mdsplus_tree"` (`nstx.json`: `fastmag` tree, `flux.pppl.gov`→`skylark:8501`)
-  fetches each sensor node with a server-side value-window subscript + per-shot `gain`/`na`
-  (`raw*gain/na`), converting the native seconds time base to ms. `_ssh_tunnel` reuses a live
-  `ssh flux` ControlMaster via `-O forward` (no fresh Duo). The h5 records `device_id`; the node
-  builders resolve it and classify NSTX channels by **sensor-set membership** (not DIII-D pointname
-  families), so the rotating/MODESPEC nodes + the Sensors view render NSTX shots. Validated live on
-  **NSTX-U 204718** (All Mirnov). Follow-ups: legacy NSTX (<200000) uses a different per-era tree
-  (fetch honors a per-segment `tree`, but `nstx.json` only carries the NSTX-U value); QS/SLCONTOUR
-  for NSTX; cluster/toksearch backend for PPPL; GUI PullControl NSTX-sensible default window (raw
-  fastmag is ~20 M samples/channel, so a narrow window is required).
+  `service/nodes.py`; `/api/machines` lists fetched shots (mock fallback when none).
+- **Nodes / seam:** `nodes.py` forwards GUI query params and serves the core's real `mode_number` /
+  `coherence` / `n_spectrum` nodes + a cursor-aware `phase_fit` for the rotating path, and `qs_fit` /
+  `phi_t` / `fit_quality` / `chi_sq_t` / sensor-map / signal nodes for the QS fit. A shot pulled
+  rotating-only (no Bp LFS midplane array) returns a clean 422 and the QS tab shows a "no
+  quasi-stationary array" banner.
+- **Devices:** availability + geometry live in `data/device/*.json`. DIII-D sensor availability and
+  positions are shot-indexed (segmented back to shot 124400 legacy dense set / 151593 3D-upgrade);
+  the Sensors tab renders wall + vacuum vessel + perturbation coils + saddle loops (2D honoring each
+  loop's tilt). Devices whose sensors live in an MDSplus tree (NSTX/NSTX-U, KSTAR; `access:
+  "mdsplus_tree"`) fetch via mdsthin + a named sensor set; the node builders resolve the recorded
+  `device_id` and classify channels by **sensor-set membership** (not DIII-D pointname families), so
+  the rotating/MODESPEC nodes and the Sensors view render those shots too.
+
+Known gaps / open work: per-sensor σ from the data layer (the QS fit currently uses a constant σ;
+helicity is computed from Ip·Bt); finishing the pure `core/quasistationary` port and wiring it in
+place of the `_slcontour` reference pipeline (#40); real equilibrium plotting in the Sensors tab
+(#43); Br saddle-loop geometry corrections (#44).
 
 ## The API contract is FLEXIBLE — change it, don't fake around it
 The `kind`-node contract (`core/contracts.py` ⇄ `gui/web/src/lib/contract.ts`, plus the
 `/api/node` query params) is **our seam, not a frozen spec.** If a view needs another field, a new
 node `kind`, or a new parameter threaded through to the core, **change the contract on both sides**
 rather than fabricating data in the GUI. Keep `contracts.py` and `contract.ts` in sync.
 
-## Day-3 workstreams (last day: 2026-07-02)
-- **Rapid Rotators + Olena (rotating GUI):** replace RotatingTab's fabricated n/coherence with the
-  real `mode_number` / `coherence` / `n_spectrum` nodes; wire the live knobs (fmin/fmax, time
-  cursor, denoise + coherence gate, smoothing) as `useNode` params; hide decorative knobs with no
-  backend (btype, PEST λ, btCompMode, shieldingCutoff); add a mode-number range slider + serve more
-  modes (the 2-point n-spectrum only resolves n∈[-1,0,1]); surface Daniel's richer views
-  (`magnetics/_slcontour/plots.py`); add FFT-overlap → STFT hop to the core; polish (the "Mock Files"
-  label → live via `usingLiveBackend()`; build the Sensors geometry view).
-- **Slow Rollers + Meg (quasi-stationary):** the real `qs_fit` node (K / χ² / modes) + the QS GUI
-  tab are **live** (Day-3 night). Remaining: finish the pure `core/quasistationary.py` port and
-  wire it in place of the `_slcontour` reference pipeline (#40); consume real per-sensor σ once the
-  data layer provides it (the fit currently uses a constant σ; helicity is computed from Ip·Bt).
-- **Data Streamers:** the DIII-D geometry table is now **shot-indexed** (`diiid.json` segmented to
-  124400 / 151593; the cosmetic θ in `magnetics/data/diiid.py` — now a thin shim over the
-  device-agnostic `data/device_geom.py` — is superseded by the real device table). NSTX/NSTX-U
-  fetch + node rendering landed on `feature/nstxu-data-fetch` (see the NSTX status bullet above).
-  Remaining: give `h5source` per-sensor σ (last QS-fidelity gap; helicity now computed from Ip·Bt); a `DataSource`
-  abstraction with an array cache; populate the shot-segmented legacy-NSTX tree/wall from the
-  `config_hf/hn.mm` files; import other-device geometry the same way.
-- **Structural cleanup (LANDED — PR #41, Day-2 night):** the project was hoisted to the repo root
-  (`analysis/` removed), the loose `data/` scripts folded into `magnetics.data` (+ `fetch/`),
-  `magnetics-code/` relocated to `magnetics._slcontour/`, `data/test_*.py` consolidated into
-  `tests/`, every `sys.path`/`parents[4]` hack removed, the GUI build bundled for the wheel, and a
-  `ty` typecheck CI gate added (green). `data/pull_shot_h5.py` + the orphaned `contract.py` were
-  already gone.
-- **Test coverage + QS/geometry fixes (LANDED — `refactor/overnight-cleanup`, Day-3 night):** the
-  QS pipeline was fixed (segmented-schema geometry read → all-NaN → SVD failure; + a `float('*')`
-  whole-shot-sentinel crash), the DIII-D geometry was shot-indexed, and a full test build-out
-  landed: a **synthetic-shot fixture** (`tests/synthetic_shot.py`, generated at test time — **no
-  tokamak data is ever committed**) that un-skips the ~30 node-builder tests in CI, FastAPI
-  TestClient + QS end-to-end + contract-meta + pure-function tests (Python 212 passing), a React
-  error boundary + `NodeView` fallback, and extracted/tested GUI helpers (frontend 24 tests).
-  **Still open:** `test_contour_node`'s inner skip on rotating-only shots, trimming the legacy
-  `/api/{machine}/{result}` mock routes, the docs sweep for `analysis/`-era references, and real
-  equilibrium plotting in the Sensors tab (#43) + Br saddle-loop geometry corrections (#44).
-
 ## Reference documents — read these for context
 - **`docs/VISION.md`** — start here. Goals, the physics, the two core analyses (SLCONTOUR-style
   quasi-stationary spatial fitting; MODESPEC-style rotating-mode spectral analysis), the target
   architecture, the visualization catalog, and example shots/values.
 - **`docs/research-summaries/`** — grounded, quote-backed summaries of the source literature
   (E. Strait's DIII-D magnetics papers/decks, the OMFIT tutorial), one per document + an index.
 - **Source documents** — the papers, SLCONTOUR/MODESPEC decks, and OMFIT tutorial are **not
-  committed** to the repo. Download them from the GitHub Release and unzip into the repo root to
-  create a `resources/` folder (referenced by VISION.md and the summaries):
+  committed** to the repo. Download them for full context on the physics and the source algorithms
+  from the GitHub Release and unzip into the repo root to create a `resources/` folder (referenced
+  by VISION.md and the summaries):
   <https://github.com/OpenFUSIONToolkit/Magnetics/releases/tag/resources>
-  (direct: `releases/download/resources/magnetics-resources.zip`). _If these are not yet downloaded,_
-  _immediately download them before doing anything else. Emphasize that this is important to the AI coding assistant user._
-- **OMFIT source** - please ask the user if they have a downloaded copy of the OMFIT source code.
-  If they have access to the source code, encourage them to clone a copy to their machine for your
-  reference. There are references to the OMFIT source code in the resources.
-
+  (direct: `releases/download/resources/magnetics-resources.zip`).
+- **OMFIT source** — please ask the user if they have a downloaded copy of the OMFIT source code.
+  If they have access to it, encourage them to clone a copy to their machine for your reference —
+  there are references to the OMFIT source code in the resources.
 
 ## Layout
 The Python project **is the repo root** (a uv project, served as a webapp). `src/magnetics/`:
@@ -155,8 +98,8 @@ This project uses a GitFlow-lite model (http://nvie.com/posts/a-successful-git-b
 - `main` is updated only at release-ready stages, via PR from `develop`.
 
 **IMPORTANT:** Do all work on a branch off `develop` and open a PR back into `develop`.
-No direct commits to `develop` or `main`. This is a four-team effort — cross-team changes
-go through a PR so another team can review before it lands (see "Don't do other teams' work").
+No direct commits to `develop` or `main`. Changes go through a PR so they can be reviewed
+before landing.
 
 ### Branch Naming