Migration to v3 (typescript + python)#25
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…init status check for FastAPI and frontend run dev connecting to it
Replace networkx/scipy/python-louvain with python-igraph (same C core as R igraph — all v2 algorithms port 1:1, see SPEC). Package management via uv: deps in pyproject.toml + uv.lock, requirements.txt deleted. Remove stale algorithms/ scaffold dirs (SPEC now uses flat service modules). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…1 complete) Dev: docker-compose with uv + node images, hot reload both sides, VITE_PROXY_TARGET for in-network proxying. Prod: multi-stage build, nginx serves Vite dist + proxies /api to uvicorn on one image (v2 r-base Dockerfile replaced; v2 preserved via v2-legacy tag). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Ports config/server_variables.R + global_variables.R into app/config.py (RColorBrewer Set3/Set1 palettes inlined as hex). Endpoint serves the v2 handler_initializeGlobals payload plus node palette, floor defaults, topology metric and no-edge-layout lists. static_variables.R was mutable Shiny state, ui_variables.R a footer year — both obsolete. All four R config files deleted. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Ports the parseUploadedNetwork() chain from functions/input.R: subset legit columns, trim, dedup (channel-aware), scale weights into 0.1..1 via mapper(), build Node_Layer keys. Validation mirrors isNetworkFormatValid() (missing mandatory columns, non-numeric weight, empty channel) as HTTP 400; MAX_LAYERS/MAX_EDGES enforced at the API boundary. 12 pytest cases incl. real aspirin_3channels.tsv fixture. input.R deletion deferred to Phase 7 (still holds JSON import, session export, attribute uploads). Added pandas-stubs; mypy target 3.12 for numpy stub syntax. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Ports functions/igraph/layout.R + general.R graph construction: - services/graph.py: channel filter, perLayer/allLayers/nodesPerLayers scopes, simplify (sum parallel weights, keep loops) - services/layouts.py: registry of all 11 v2 UI layouts as Graph.layout_* calls, per-request RNG seed (v2 set.seed(123)), returns 2D [y,z] - no-edge layouts (Circle/Grid/Random) place isolated layer nodes as extra vertices (simpler equivalent of v2 filterPseudoNetwork) 24 pytest cases. layout.R deleted; general.R kept as spec through Phase 6. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Ports functions/igraph/cluster.R. Clustering is an optional step of POST /api/layout (not a separate endpoint): detect communities (Louvain/Walktrap/Fast Greedy/Label Propagation via Graph.community_*), lay super-nodes out with the global algorithm repelled from origin, lay each community's members locally (real intra edges + tiny all-pairs edges so disconnected members spread), translate into place. Response gains a clusters map. 8 new pytest cases; cluster.R deleted. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Ports functions/igraph/topology.R: Degree (raw Graph.degree, not normalized centrality), Clustering Coefficient (weighted local transitivity, isolates=0), Betweenness (edge-direction toggle + weights). Values mapped per subgraph into [0.5, 2.5] via mapper() (constant → 1); raw values returned for the View Data table. 7 pytest cases. topology.R + general.R deleted — functions/igraph/ fully ported. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- POST /api/session/import: ports parseUploadedJSON + isJSONValid
(defaults for scene/layers/nodes/edges, channel drop, edge dedup,
scramble flag). Loads real Arena3DwebApp_aspirin.json / export JSONs.
- POST /api/session/export: thin JSON download (stateless — frontend
owns the state).
- POST /api/external + GET /api/external/{token}: session stored under
a random token in tmp/ with 24h TTL sweep + path-traversal guard;
resolves back through the same normalizer (SPEC §5).
- VR (functions/vr.R) DROPPED, not ported — depended on external
bib.fleming.gr hosting + A-Frame, out of scope (see MIGRATION.md).
11 pytest cases. Deleted init.R, general.R, reset.R, render.R,
js_handling.R, vr.R. input.R kept: attribute-upload functions still
to port to a future /api/attributes endpoint.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Foundation singletons: - bus/index.ts: typed pub/sub, unsubscribe handle (replaces rshiny bridge) - store/index.ts: single AppState source of truth - commands/base.ts: Command + CommandHistory (undo/redo, emits history:changed) - api/client.ts: hand-written typed fetch wrappers mirroring backend Pydantic models (no codegen dependency) — network/layout/topology/ session/external 5 Vitest tests; tsc + eslint clean (skipLibCheck for third-party stubs). Verified live: config/network/layout return 200, OpenAPI exposes all 9 paths. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Migrate Scene/Layer/Node/Edge from www/js/classes/ to typed frontend/src/three/ on npm three r170. Key finding: vendored www/js/three/three.js was byte-identical to stock Three.js r117 (diff = only a missing trailing newline). SPEC's "manually patched copy" claim is wrong — no core patches exist, so no src/three/ subclasses were needed. - constants.ts: static geometry + 280-color palette (verbatim from v2) - runtime.ts: typed ctx singleton replacing v2 ambient globals (registries, screen bounds, edge tunables, color-priority flags). nodeGroups/layerGroups were new Map() but only bracket-accessed in v2 -> typed as plain records. - Scene/Layer/Node/Edge.ts: faithful ports; only API change is THREE.Math -> THREE.MathUtils. - three.test.ts: 16 Vitest tests across all four classes. Deferred (ponytail-marked): Scene.rotate() DOM slider + Shiny glue and Layer.getColor() picker DOM read -> Phase 11 canvas_controls. Delete www/js/classes/ + three.js. Keep matrix4.js/drag_controls.js as living spec until Phase 11. tsc + eslint + prettier clean; 21/21 vitest pass. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Implement the 8 Command classes in src/commands/scene.ts, each capturing before/after state on the Phase 9 Three.js object model so CommandHistory can undo/redo: - ChangeNodeColorCommand / ChangeNodeSizeCommand - ChangeEdgeColorCommand (captures colors + edgeFileColorPriority) - MoveLayerCommand (position/rotation/scale; redraws inter-layer edges) - ApplyLayoutCommand (positions + optional cluster IDs/colors, one step) - ApplyTopologyCommand (node scales) - ChangeThemeCommand (store-only via injected getter/setter) - LoadNetworkCommand (build closure + ctx registry snapshot for undo) Commands are thin: they apply/reverse already-decided values. API fetch and position/scale math is the Phase 11 actions' job, which will construct these commands with the results. Supporting changes: - runtime.ts: add ctx.edgeObjects registry + snapshotRegistries / restoreRegistries helpers (RegistrySnapshot). - bus: add layer:moved event. 9 Vitest tests (execute/undo/redo per command). tsc + eslint clean; 30/30 tests pass. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Port the portable, unit-testable slice of the v2 object_actions: src/actions/layout.ts — executeLayout coordinate normalization plus applyLayout / applyTopology, which fetch from the API and dispatch the Phase 10 ApplyLayoutCommand / ApplyTopologyCommand (one undo step each). Confirmed against backend: /api/layout returns raw igraph [y,z] coords (no layer-width normalization), so the frontend still performs the v2 mapping into [-minWidth/2, minWidth/2] * layer scale. Topology scales are already mapped server-side and applied verbatim. Re-scope the rest of Phase 11: the remaining 9 action files are coupled to the renderer, camera, animate() loop, raycaster, DragControls, CSS2D labels, and the UI panels — all built in Phases 12-13. They move to those phases (documented in PLAN.md) rather than being stubbed now, and www/js/object_actions/ deletion moves with them. ponytail: allLayers scope only; perLayer/local layout refinements deferred to the Phase 13 scope UI. 5 Vitest tests (normalize + applyLayout + applyTopology). tsc + eslint clean; 35/35 tests pass. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Stand up the render spine so the app draws its first pixels. Verified
live with playwright-cli: /api/config loads, the WebGL canvas mounts,
and the tilted coordinate axes render.
- src/actions/screen.ts: port of screen.js — renderer, camera
(orthographic), window bounds, raycaster, FPS-limited animate() loop.
Shiny sync calls dropped. (screen.js was deferred out of Phase 11 for
exactly this dependency.)
- src/main.ts: port of on_page_load.js — config fetch -> renderer/
camera/scene setup -> mount canvas into #app -> animate. Exposes
window.__arena = { ctx, history } so Playwright can read 3D scene
state via page.evaluate (WebGL is opaque to the a11y tree).
- src/event_listeners.ts: window resize + Ctrl+Z / Ctrl+Shift+Z /
Ctrl+Y undo/redo wired to CommandHistory.
- src/utils.ts: port of general.js (pure helpers), 6 Vitest tests.
- runtime.ts: add ctx.renderer/camera/fps + screen bounds (persist
across network reloads; not reset by resetContext).
Deleted www/js/general.js (fully ported + tested).
Deferred: the canvas mouse/keyboard scene controls (clickDown/Drag/Up,
sceneZoom, keyPressed, right-click) land with canvas_controls (still in
the Phase 11 list). Documented in PLAN.md.
Updated PLAN.md Phase 13 to drive/verify DOM panels with playwright-cli
(@playwright/cli, installed) against the window.__arena hook.
tsc + eslint clean; 41/41 vitest pass.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…artial) buildNetwork consumes backend-parsed NetworkData: fresh Scene + ctx registries, layers spread on x, nodes scrambled per layer, edges grouped per src---trg pair with channel colors. loadNetwork wraps it in LoadNetworkCommand so an upload is one undo step. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Port of www/js/object_actions/node.js pure parts: raycaster hover, double-click/search/select-all selection synced to the store, repaintNode (cluster branch folded into Node.getColor), label-flag priorities using Layer.isVisible instead of DOM checkboxes, shape/color-priority setters. scrambleNodes moves here from network.ts. ctx gains lastHoveredNodeIndex, selectedNodeColorFlag and the two node-label flags. DOM-bound pieces (search bar, sliders, lasso, node description div, attribute upload) stay with canvas_controls.ts / Phase 13 UI. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
… 12 partial) Port of www/js/object_actions/edge.js pure parts: renderInterLayerEdges now runs every animate() tick (remove while dragging/paused/invisible, v2 locked-flag redraw pair), channel color/visibility, unselectAllEdges, and the edge-setting setters (direction, arrow sizes, width-by-weight, opacities, color priorities, curvatures). redrawIntra/InterLayerEdges move here from commands/scene.ts private helpers. ctx gains the four inter-layer render flags. Channel UI lists/picker stay with Phase 13; edge attributes upload with POST /api/attributes; edge build already lives in network.ts. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…12 partial) Port of www/js/object_actions/layer.js pure parts: initialSpreadLayers moves here from network.ts, raycaster hover with red highlight + repaint, double-click/selectLayer/select-all selection synced to the store, repaintLayers with default/picker color priority, per-layer visibility and node-label toggles that recompute node label flags, plus the coords/opacity/wireframe/color-priority setters. ctx gains lastHoveredLayerIndex, hoveredLayerPaintedFlag, renderLayerLabelsFlag. Checkbox group + color-picker DOM stay with Phase 13; DragControls and the held-key/slider rotate/move/scale intervals with canvas_controls.ts. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Port of www/js/object_actions/themes.js: THEMES presets (light/dark/gray from the v2 buttons), applyTheme sets renderer clear color, ctx.edgeDefaultColor/labelColor, reassigns channel colors from the config palette and repaints layers picker-priority with the theme floor color. registerThemeListener() subscribes to theme:changed in main.ts, so ChangeThemeCommand execute/undo now performs the concrete recolour. Supporting: ctx.labelColor (v2 globalLabelColor), repaintLayers gains an optional pickerColor override, assignChannelColorsFromPalette lands in edge.ts. Theme buttons DOM + channel edit list stay with Phase 13; label recolour with labels.ts. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Port of www/js/object_actions/labels.js keeping v2's plain absolutely-positioned divs in #labelDiv (no CSS2DRenderer dep; inline position styling until the Phase 13 stylesheet). createLabels runs on network build; flag-gated renderLayerLabels/renderNodeLabels register as animate hooks via a new registerAnimateHook in screen.ts, which avoids a screen->labels->node->screen import cycle. showLayer/NodeLabels modes, label resize and setLabelColor ported; themes.ts now recolors labels on theme change and decideNodeLabelFlags raises the node render flag as v2 did. ctx gains renderNodeLabelsFlag + the two layer-label flags. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Port of the canvas half of www/js/event_listeners.js plus the held-key and lasso helpers it pulled from node.js/layer.js: wheel zoom, z/x/c axis keys + arrow-key pan (modern event.key), clickDown/Drag/Up with left-drag pan, middle-drag orbit, held-key node-translate/layer-rotate, shift-lasso rectangle select (dim to 0.5, select on mouse-up), and dblClick with v2's node -> layer -> unselect-all priority. registerCanvasControls() wires the listeners onto the mounted canvas from main.ts (tabIndex for keydown, scroll/autoscroll prevention, mouseleave button release). Shiny syncs and 100ms debounces dropped. Right-click node menu stays with right_click_menu.ts; DragControls layer dragging and the nav-button/slider table with Phase 13. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…artial) Port of www/js/object_actions/right_click_menu.js plus the context-menu builder from event_listeners.js: selectNeighbors, selectMultiLayerPath (v2 starting/current-layer exclusions), recursive selectDownstreamPath over inter-layer edges, and the executeCommand tail (render flags, label flags, store sync). The <select> menu is placed over the clicked node in #labelDiv; Link opens the node URL. Wired to the canvas contextmenu event and removed on clickUp in canvas_controls, as v2 did. Loader spinner + description panel content stay with Phase 13 UI. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…x4.js Hand-port of v2's tweaked three.js DragControls copy onto npm three math (the matrix4.js shim goes away). v2 behavior kept: drag engages only while the left button is held over a hovered layer plane, label render flags raised while dragging, camera-facing drag plane with parent-space offset. On release it now raises the inter-layer edge render flag and emits layer:moved (v2 routed this through Shiny syncs). The planes list is read live from ctx so a single registration survives network reloads (v2 recreated DragControls per load). Registered from main.ts. Both v2 living-spec files deleted; MIGRATION.md rows ticked. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…ject_actions) screen.js, labels.js, themes.js, right_click_menu.js, event_listeners.js and on_page_load.js are fully covered by the ported TypeScript actions and main.ts; MIGRATION.md rows ticked. Kept as living spec for their unported remainders: layout.js (predefined/star/cube layouts), network.js (importNetwork session JSON), node.js/edge.js/layer.js/canvas_controls.js (Phase 13 DOM), config/, rshiny_handlers.js/rshiny_update.js (map to Phase 13 panels). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
buildFromSession consumes the backend-normalized SessionData (now typed in api/client.ts): scene position/scale/rotation + renderer clear color, full layer transforms (initial spread only when the backend generate_coordinates flag says the JSON carried none), nodes with positions/scale/color/url/descr (scramble per flag within min layer width), edges with per-row file colors and opacity as the weight, and the v2 setJSONExtras flags (label color, direction, width-by-weight, edgeFileColorPriority). loadSession wraps it in LoadNetworkCommand as one undo step. createEdgeObjects gains the v2 decideEdgeColors rule: a row's own color wins over the channel palette. The store receives a NetworkData equivalent so later layout/topology calls work on imported sessions too. network.js is now fully ported and deleted; MIGRATION.md ticked. Session export + File-panel wiring land with Phase 13. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Ctrl+Z with the canvas focused armed axis-transform mode; a following drag moved nodes/layers unintentionally. Skip axis arming on modified keydowns. Closes L3 in PLAN.md. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The module-local currentTheme shadowed store.currentTheme, which was never written. Route the ChangeThemeCommand getter/setter through the store so there is one source of truth. Closes L4 in PLAN.md. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
An edge channel missing from ctx.channelColors produced new THREE.Color(undefined) -> silent white. Fall back to the edge default color. Closes L5 in PLAN.md. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Reading it at import time froze the value; env changes (redeploy, tests) were ignored. Read it inside the handler. Closes L6 in PLAN.md. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The native option popup rendered with the OS default light background while inheriting light --arena-text, leaving layout/clustering/topology select options light-on-light. Set an opaque dark background on .form-select option/optgroup. Closes U1 in PLAN.md. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
V3 fable auto
uv audit: no known vulnerabilities. 62 backend tests pass. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Majors: three 0.170→0.185, typescript 5→6, eslint 9→10, vite 6→8, vitest 2→4, typescript-eslint 8.58→8.62, plus playwright/prettier/@types. Fallout fixed: - add src/vite-env.d.ts (TS6 now errors on untyped CSS side-effect imports) - drop redundant type assertions flagged by newer typescript-eslint/@types/three 107 unit tests pass, tsc + eslint clean, build succeeds. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Feat satellite view
raycasting undraggable layer bug finally fixed!
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Full rewrite: migrated from R/Shiny to a FastAPI (Python) backend + Vite / TypeScript / Three.js frontend. Algorithms (layouts, clustering, topology) ported 1:1 via python-igraph.
Added
?session=URL (POST /api/external).Changed
Fixed