CHANGELOG.md

Changelog

1.141 — 2026-06-11

Map-first default view + fill the canvas to the bottom.

• Results table collapsed by default. The explorer now boots map-first — the Edges/Nodes table starts collapsed to its bottom bar (click to expand), giving the network the full height. Expanding/maximizing still works as before.
• No more bottom dead band. The layout reserved a 56px topbar height that this (topbarless) layout never renders, so the sidebar and canvas stopped short of the viewport bottom. The workspace now fills the full height, and the collapsed-results reserve was trimmed to match the fixed bar — the canvas meets the results bar flush and the left rail extends all the way down.

1.140 — 2026-06-11

Fix: ~30s blank canvas on the first analysis after a cold start.

• The WIPER/WINNER engines are numba-JIT-compiled; the first /api/analyze after a server start paid a one-time ~30-40s compile, during which the explorer canvas sat blank.
• The server now pre-compiles those kernels in a background daemon thread at boot (a tiny throwaway analysis), so the first real page load is fast (~2s). The server still accepts connections immediately while warming — serving is never blocked — and the warm-up is best-effort (any failure is swallowed). Network-only, no behavior change.

1.139 — 2026-06-11

Fix: http://localhost:<port> served a blank page.

• The server bound IPv4 127.0.0.1 only, but localhost often resolves to IPv6 ::1 first (notably on macOS), so a localhost tab got connection-refused and rendered nothing — only 127.0.0.1 worked.
• The server now binds both loopback families (127.0.0.1 and ::1) by default, so localhost works regardless of resolution. It stays loopback-only (no LAN exposure) and falls back to IPv4 alone if IPv6 is unavailable. Non-loopback --host values bind once, unchanged.

1.138 — 2026-06-11

Left size dock — legends and their controllers, off the canvas.

• The node-size and edge-size legends plus their controllers now live in a collapsible left panel docked beside the canvas (not floating over it), so the network gets the full remaining width.
  • Edge size card: edge-score controller (Raw / WIPER1 / WIPER2, UFC / W, Linear / Log₂) + the edge-width legend.
  • Node size card: node-radius controller (Linear / Log₂, Relative / Absolute, min, ratio slider) + the node-size legend.
• These controllers were moved out of the gear popover (single home). The gear keeps Layout, Edges shown, Nodes shown, Declutter, and the Side-panel toggle.
• A ‹ / › handle collapses the dock to a thin rail; the gear's Side panel switch hides it entirely for maximum canvas.

1.137 — 2026-06-11

Follow-ups to the explorer readability features.

• Header count badge now reflects the current view. N/total nodes, M/total edges shown is recomputed from what is actually drawn after filtering and off-screen culling, and updates on every pan/zoom (not just on filter changes). Zooming in now shows e.g. 15/34 nodes, 22/78 edges.
• Legends are user-toggleable. New Legends switch in Network Display shows/hides the node-size and edge-width legends on the canvas (default on).
• The node-size control (the ratio slider under Node radius) lives in the Network Display popover (gear icon) — unchanged, just clarified relative to the on-canvas legends.

1.136 — 2026-06-11

Two explorer readability features (Network Display settings).

Node size ratio + zoom-steady sizing

• New ratio slider (1–100) under Node radius sets the largest-to-smallest display ratio directly: the smallest node holds the min radius and the largest is min × ratio. (Replaces the old ×fold field; relative mode.)
• Node glyph sizes now stay visually steady as you zoom — radii, edge stroke widths, and labels are counter-scaled by 1/zoom, so zooming changes only spacing, not marker/label sizes. At fit (zoom = 1) rendering is unchanged. The min/max px inputs apply in Absolute mode; the ratio slider in Relative mode (controls auto-show per mode).

Off-screen culling (declutter)

• New Declutter toggle (on by default): when zoomed in, any node whose center falls outside the viewport is hidden, along with every edge that touches it — cutting edge clutter. At fit / zoomed-out the viewport covers the whole graph, so nothing is culled. Recomputed on every pan/zoom.

1.135 — 2026-06-09

Assistant copilot: offline fallback so queries still work when the shared agent service is down.

• A free-form network-analysis request ("analyze the network", "rank the top hubs", "top 5 important nodes") used to just error if the agent service (:8088) was unreachable. It now falls back to SPINNER's own WIPER / WINNER engines: it summarizes the on-screen results, or re-runs POST /api/analyze on the current edge list, and returns the top nodes by WINNER leverage plus the top WIPER2 edges. A ↺ agent service offline note marks the local run, and top N is honored.
• Stays network-only — the fallback uses no expression data, no API key, and no LLM. Drug-target ranking (importance × cross-cell selectivity) still requires the agent service + GeneTerrain; the reply says so.
• Non-analysis requests still show the "start run.sh" notice.

1.134 — 2026-06-08

Assistant copilot: fix the panel flickering on open and on each reply.

• No more message churn. A reply (or an error) used to be drawn by adding a … placeholder bubble and then removing it to add the real message — a visible add/remove flash, especially fast when the agent service is unreachable. The placeholder is now a single persistent bubble that is rewritten in place into the first text, tool note, or error, so the message count never dips. The indicator animates via a new .chatMessage.thinking style.
• Smoother drawer slide-in. The Assistant drawer is promoted to its own compositor layer (will-change: transform), removing the repaint flicker during the open animation.
• Unrelated to the UI, the failed-query message already points at the cause: the shared agent service (run.sh, default :8088) must be running for free-form requests — terse UI commands still work offline.

1.133 — 2026-06-07

Fix: collapsing the results table left no way to restore it (the collapsed row shrank to ~2px and the header was clipped/off-screen). The collapsed state is now a fixed bar pinned to the viewport bottom — always visible, labeled N / N edges · click to expand, and restored by clicking anywhere on it (or the chevron). The workbench reserves bottom padding so the canvas isn't hidden behind the bar.

1.132 — 2026-06-07

Results table redesign for usability.

• The Edges/Nodes table now scrolls internally within a fixed-height region (default ~7 rows, sticky headers) instead of growing the page — which had made it look like a 2-row table.
• New header controls: a row-count chip (78 / 78 edges, (filtered) when a filter is active), a maximize / restore toggle (table fills the workspace, canvas shrinks to a strip), and a collapse / expand toggle (header only). The drag-resize handle still works.

1.131 — 2026-06-07

Copilot fix: the Assistant now operates on the currently-loaded network.

• The Assistant sends the UI's current edge list to the agent service, so "analyze the network / this network / the current network" runs spinner_analyze on what's on screen (previously the stateless service had no knowledge of the loaded graph and replied "no network analyzed yet").
• The local-vs-copilot router no longer treats analyze / geneterrain / rescore as local UI commands — those reach the copilot; pure UI toggles and routing stay local.

1.130 — 2026-06-07

Assistant copilot. The Assistant drawer can now drive the full SPINNER → GeneTerrain drug-target workflow via a shared LLM agent service.

Assistant copilot (app.js, index.html, styles.css)

• Free-form requests ("analyze this network and rank monocyte drug targets, then give me a GeneTerrain link") stream to a shared agent service (Grok-backed; default http://127.0.0.1:8088, override via ?agent= or localStorage.agentBase). Tool activity renders as compact notes; a GeneTerrain target-map link renders as a clickable result.
• Direct, terse UI commands (WIPER1/2, top N, layout, plan trip, generate, geneterrain, analyze) still run locally and instantly — the router only sends sentence-like requests to the copilot.
• Graceful in-panel notice if the service is unreachable.
• SPINNER stays network-only: the LLM and the API key live entirely in the shared agent service, never in SPINNER. See the spinner-agent-console repo for that service.

1.120 — 2026-06-07

GeneTerrain interoperability. SPINNER remains network-only; this release adds a one-click bridge to the standalone GeneTerrain (GTKM) drug-target map.

Open in GeneTerrain (app.js, index.html)

• New Export → "Open in GeneTerrain" button: serializes the current WINNER node scores (the network-leverage / potency layer) as a gene\tscore TSV, base64-encodes it, and opens GeneTerrain's Targets view with the data in the URL fragment — …/?view=targets#net=<base64 TSV> — so no hosting is needed.
• GeneTerrain fuses that leverage layer with a SIGnature gene-importance matrix to rank drug targets by potency × importance × cross-cell selectivity.
• The GeneTerrain base URL is asked once and remembered in localStorage.
• The same #net= / ?net= contract is agent-operable directly from /api/analyze output — one workflow, two front doors (human button / agent URL).
• No expression or attribution data enters SPINNER's scoring. Documented in docs/INTEGRATION.md §3.

1.110 — 2026-06-03

Deep-link data loading and dense-graph robustness. Builds on the 1.100 redesign; the POST /api/analyze contract is unchanged (additive summary fields only).

Deep-link loader (app.js)

• Launch SPINNER with an external dataset at boot, in precedence order:
  • embedded hash payload — #data=<base64 JSON>, #edges=<base64 TSV>, or #text=<URI-encoded TSV> (self-contained link, no hosting needed);
  • ?edges=<url> — fetches a tab-separated edge list cross-origin (good for large datasets);
  • postMessage({type:'spinner:load', ...}) from a parent frame, with a spinner:loaded acknowledgement.
• Query options honored alongside all paths: ?title=, ?iterations=, ?novel=1. A failed fetch falls back to the demo network with a chat notice.

Dense-graph robustness (webapp.py)

• WIPER1, WIPER2, and WINNER are scored independently and each guarded against (RuntimeError, MemoryError, OverflowError), so raw edges plus whichever engines succeed always return instead of failing the whole request. The response carries summary.warnings and per-engine wiper1Available / wiper2Available / winnerAvailable flags, plus an optional maxPathsPerPair request parameter.
• Recursion limit and request-thread C-stack raised so deep-but-bounded WIPER path enumeration completes on mid-size graphs.

Edge rendering (app.js)

• Edges fall back to raw weight for width, filtering, and ranking when the selected WIPER metric is unavailable, so a degraded graph still renders its edges instead of showing none.

1.100 — 2026-05-08

Full GUI redesign of the SPINNER explorer, delivered as a Claude Design handoff bundle. The Python backend (POST /api/analyze) and served filenames are unchanged; the JavaScript contract is preserved.

New explorer chrome

• Map-first canvas in the spirit of Google Maps: floating search box top-left, gear + fullscreen stack top-right, + / − zoom stack bottom-right.
• Gridded SVG canvas (20 px fine, 100 px major) that pans and zooms with the graph; light- and dark-mode aware.
• Status badge in the header reports nodes shown / total · edges shown / total.
• Polished scientific palette — IBM Plex Sans/Mono, warm-paper surfaces, tabular numerals, fine 1 px borders, dark mode preserved.

Sidebar workflow

• Collapsible left nav with icon glyphs for Build, Results, Export, Tidy, Assistant. Sidebar starts collapsed; the SPINNER icon doubles as the home / expand control.
• Build panel merges the former Input and Generate steps. Synthetic graph controls (Random / Scale-free, node count, edge count, w_min / w_max) sit above file upload, paste-edge-list, project name, iterations, device, and the WIPER1 novel-edge toggle.
• Tidy wipes node positions, re-seeds, and re-runs the force-directed simulation, then resets zoom to fit.

Network generation & layout

• One-click synthetic network generation (Random or scale-free); page boots with a default scale-free graph (34 nodes, 78 edges, w ∈ [0.10, 0.95]).
• Force-directed layout reworked for short, balanced edges:
  • Springs target a short rest length scaled by edge weight; spring stiffness scales with weight so strong ties cinch tight.
  • Repulsion is a soft, short-range 1/r² push scaled by node radii.
  • Hard collision boost prevents overlap.
  • The Iterations input now caps the simulation; no ticks are skipped.
• DEMA, Force, and Organic layout modes are all selectable from the settings popover.
• overflow: visible on the SVG so edges connected to off-canvas nodes no longer vanish during pan / zoom.

Search

• Map-style search box with shadowed pill input; results dropdown only renders while the field is focused.
• Matched nodes and edges glow with the accent color and pulse softly; the rest of the network dims to ~15 % so matches stand out.

Directions / route planning

• Google Maps-style directions card slides down from beneath the search bar. Travel-mode tab strip across the top — Hops · Raw · W1 · W2 — with a blue underline on the active mode and a borderless circular close X.
• From / to inputs flank a vertical rail (origin dot → dotted line → destination square) with a circular swap button that rotates 180 ° on hover.
• Routes auto-compute as inputs change. Path costs use −log p summation over edge probabilities (raw weight, WIPER1 weight, WIPER2 weight) so shortest paths reflect real probabilistic cost.
• Selected route highlights in red (#e23b2b, dashed) with the selected leg in deeper red; non-route edges, nodes, and labels all dim out.
• centerRoute reserves a left-side gutter for the directions card and fits the entire highlighted path inside the remaining viewport, without obstructing the route.
• Per-leg detail rows show p, −log p, the running Σ −log p and Π p.

Network display settings

• Settings popover with dedicated controls for:
  • Layout — DEMA / Force / Organic.
  • Edge score — Raw / WIPER1 / WIPER2, with UFC / W sub-toggle and Linear / Log₂ scaling. Default edge score is W.
  • Edges shown — All / Top N / Top % / ≥ score. The number row collapses to just the input relevant to the active filter mode.
  • Nodes shown — same All / Top N / Top % / ≥ score pattern.
  • Node radius — Linear / Log₂ × Relative / Absolute, plus min, max, and relative-fold inputs.
• Selection details follow the active metric: edge cards show only the selected score, rank, initial value, and reason; node cards show their incident edges using the active metric.
• Edge widths now span roughly an 11 × ratio (≈ 0.8 px → 8.8 px) with a t^1.5 curve so weak ties stay as hairlines and strong ties read clearly.
• Selection details and the "Show selection details" pill stay hidden until the user clicks a node, edge, or search result.

Assistant

• Right-side slide-over drawer with a scrim, opened from the Assistant nav item. Esc, scrim click, and the × button all close it.
• Composer with ⌘ ⏎ to send hint; the assistant copilot can be wired to network generation, ranking, and route planning prompts.

Results & export

• Results table with Edges / Nodes tabs, sticky headers, monospace numerals, row filter input, and a left indigo bar on the selected row.
• Export panel covers Geneterrain, SVG visualization, shown-network TSV, edge / node tables, Notion (.md), Word (.doc), and Excel (.xls).

Reliability

• Client-side fallback for POST /api/analyze synthesizes plausible WIPER1 / WIPER2 / path-load values when the Python backend is unreachable (e.g. opening index.html directly), so the explorer always renders a network in static previews.

0.1.0 — initial release

• Core SPINNER pipeline: WIPER1, WIPER2, WINNER scoring with path-flow pathload, served by a small local http.server web app at POST /api/analyze.
• Plain HTML/CSS/JS frontend with a network explorer, ranking tables, and TSV / SVG export.