Migration to v3 (typescript + python) - #25

Merged

vagkaratzas merged 173 commits into

mainfrom

Jul 27, 2026

Commits on Apr 6, 2026

migration spec and plan init
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scaffolding front- and backend folder structure + config files init, init status check for FastAPI and frontend run dev connecting to it
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Commits on Jul 2, 2026

plan, spec and migration docs revised and updated with Fable 5, serena init
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backend: switch to uv + python-igraph

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infra: docker-compose, prod Dockerfile, nginx, CI, pre-commit (Phase 1 complete)

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backend: GET /api/config + typed frontend client (Phase 2 complete)

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backend: POST /api/network TSV parser + validation (Phase 3)

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backend: POST /api/layout with 11 igraph layouts (Phase 4)

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backend: clustered layout via supernode strategy (Phase 5)

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backend: POST /api/topology metrics + node scaling (Phase 6)

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backend: session import/export + external API (Phase 7)

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frontend: EventBus, store, command history, typed API client (Phase 8)

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Commits on Jul 3, 2026

frontend: Three.js classes ported to TypeScript (Phase 9)

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frontend: undo/redo scene commands (Phase 10)

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frontend: layout/topology actions + Phase 11 re-scope (Phase 11 partial)

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frontend: Three.js render loop + main entry (Phase 12 partial)

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serena switched to python + ts
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frontend: network build action feeding LoadNetworkCommand (Phase 12 partial)

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frontend: node action — hover, selection, repaint (Phase 12 partial)

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remove ci tests from this branch
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fix frontend lint
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frontend: edge action — inter/intra render machinery + setters (Phase 12 partial)

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frontend: layer action — spread, hover, selection, visibility (Phase 12 partial)

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frontend: themes action listening to theme:changed (Phase 12 partial)

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frontend: labels action rendering in the animate loop (Phase 12 partial)

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frontend: canvas mouse/keyboard scene controls (Phase 12 partial)

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frontend: right-click node menu + path-selection commands (Phase 12 partial)

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85a2728
frontend: layer DragControls port; delete v2 drag_controls.js + matrix4.js

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chore: delete fully-ported v2 JS (event_listeners, on_page_load, 4 object_actions)

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frontend: session import build (v2 importNetwork); delete network.js

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frontend: predefined layouts — parallel, zigZag, starLike, cube (Phase 12 partial)

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frontend: session export action (v2 convertSessionToJSON)

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frontend: Bootstrap 5 navbar + tab panes in index.html (Phase 13)

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frontend: Home panel port (views/home.R) + panel overlay CSS

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frontend: File panel port (views/file.R) — upload/session/example

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frontend: Layer Selection & Layouts panel port (views/layouts.R)

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frontend: Scene Actions panel port (views/scene.R)

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frontend: Layer Actions panel port (views/layer.R)

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frontend: Node Actions panel port (views/node.R)

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frontend: Edge Actions panel port (views/edge.R + edges.R toggles)

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frontend: FPS panel port (views/fps.R)

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frontend: View Data panel port (views/data.R + render.R tables)

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docs: mark View Data panel + edges.R done in PLAN/MIGRATION

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frontend: Help panel port (views/help.R → src/ui/help.ts)

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frontend: footer port (views/footer.R → index.html static footer)

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frontend: Undo/Redo navbar buttons wired to CommandHistory

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style: prettier pass on ui panels

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frontend: retire Shiny JS bridge (rshiny_handlers/update, www/js/config)

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cleanup: delete v2 UI shell (views/, ui.R, server.R, arena3dweb.css, edges.R)

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frontend: nav controls port (canvas_controls.js nav buttons + control table)

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feat: node/edge attribute-file uploads (POST /api/attributes)

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cleanup: delete dead R/Shiny startup files (global.R, Rprofile.site, .Rproj)

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cleanup: relocate backend test fixtures, delete www/

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docs: rewrite CLAUDE.md for the FastAPI + Vite/TS/Three.js stack

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docs: rewrite README for the FastAPI + Vite/TS/Three.js stack

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docs: fix production image run port (8080:8080)

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test: Playwright E2E network flow + fix tsc stray-emit

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checking stale item of plan
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init prompt
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Commits on Jul 4, 2026

remove prompt file
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removed plan files
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feat(three): cap device pixel ratio and prefer high-performance GPU

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feat(three): drive render loop with pure rAF + timestamp FPS cap

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feat(three): dispose GPU resources of discarded redo snapshots

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feat(three): smooth eased wheel zoom with reduced-motion fallback

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feat(three): smoother pan/orbit/lasso with finer drag threshold

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fix(three): stop leaking lasso geometry/material on every drag move

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perf(three): coalesce hover raycasts to one per rendered frame

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fix(three): non-recursive raycasts in hover and double-click picking

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feat(three): optional subtle bloom via EffectComposer

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feat(ui): cohesive dark chrome for canvas overlays, footer and loader

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docs: add REPORT_THREEJS.md summarizing the Three.js/UI refinement pass

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feat: default render loop to 60 FPS

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fix(three): layer drag failing when the ray hit a plane child first

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fix(three): keep inter-layer edges live during drags

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fix(three): reposition DOM labels when the scene transform changes

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fix(three): select the hovered plane directly on layer-drag start

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fix(three): redraw inter-layer edges on scene pan/orbit/zoom

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b661d64
Merge pull request #20 from Pavlopoulos-Lab/three-js-lifting
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init prompt
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remove prompt file
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feat(ui): unified dark instrument design foundation

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feat(ui): open action panels as a side drawer, not full-scene overlay

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feat(ui): make panel content fit the drawer width

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feat(ui): redesign Home panel with hero, action cards, quiet citations

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feat(ui): theme the Help panel tab bar and content for dark mode

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feat(ui): polish scene overlays and add a centered empty state

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feat(ui): responsive nav and drawer clearance

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docs: add REPORT_TASTE.md summarizing the UI/UX redesign

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feat(ui): redesign nav help as a shortcut cheat-sheet with kbd keys

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feat(ui): polish canvas controls table with hover states and themed sliders

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fix(ui): stop nav-control button clipping and dead info scrollbar

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feat(ui): real stop/play and up/down icons on nav toggle buttons

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feat(ui): add collapse handle for side-opening action panels

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feat(network): seed node scatter so loads are reproducible

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feat(ui): collapse the File drawer after a successful load

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feat(ui): port v2 theme bar (Light/Dark/Gray) with e2e test

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fix(ui): keep theme floor color on layer hover-exit

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report removed
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Merge pull request #21 from Pavlopoulos-Lab/taste-skill-ui-ux-update
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docs: add code review report of potential bugs

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docs: add fix plan for code review findings

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fix(session): wire external session handoff via ?session= token

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fix(session): validate referential integrity on import

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fix(edge): toggle channel visibility by tag, not positional index

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fix(session): surface channel-removal warning to the client

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fix(session): reject duplicate layer names on import

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fix(session): resolve edge endpoints from node list, not id slicing

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fix(clustering): repel super-nodes radially even at x == 0

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fix(external): tolerate concurrent sweep/resolve race in _sweep

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fix(topology): score single-edge layers instead of skipping them

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fix(edge): copy colors into importedColors instead of aliasing

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fix(canvas): track lasso membership in a set, not opacity sentinel

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fix(events): don't hijack Ctrl+Z/Y while typing in inputs

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fix(canvas): ignore z/x/c axis keys when Ctrl/Meta is held

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fix(themes): back theme state with the store, drop duplicate

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fix(edge): fall back to default color for unknown channel

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fix(external): read ARENA_PUBLIC_URL per request

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fix(ui): make dropdown options readable (dark bg, light text)

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removing md reporting files
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linting / formatting
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Merge pull request #22 from Pavlopoulos-Lab/v3-fable-auto
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chore(deps): bump numpy 2.5.1, uvicorn 0.50.0

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chore(deps): update frontend deps to latest

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Commits on Jul 5, 2026

Command design pattern to add more undo/redo events
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fix Z key + node drag, labels following
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satellite view
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hide hidden layers from satellite
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Merge pull request #23 from Pavlopoulos-Lab/feat-satellite-view
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anchor zoom to mouse instead of scene middle
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raycasting undraggable layer bug finally fixed!
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Merge pull request #24 from Pavlopoulos-Lab/fix-layer-drag-always
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CHANGELOG.md init
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testing e2e failing test on github
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retry playwright test pass on github ci
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another attempt with dispatchEvent
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logos updated
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c3abd05
rename back to Arena3D
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fix httpx backend test warning by updating to httpx2
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README.ms updated
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release date added to CHANGELOG.md
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Commits on Jul 6, 2026

security fixes and optimization
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deployment-based fixes
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Commits on Jul 8, 2026

npx prettier fix
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Merge pull request #26 from Pavlopoulos-Lab/v3_fixes
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github link update to new repo
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keeping right-click node menu visible
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external api help page updated
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swapped to old Load Example network of 4 layers
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refresh labels on window resize
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export scene as png button
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add visible labels to the exported PNG
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Capturing labels in the frame
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pointer-events none above label names, to properly use lasso and layer dragging without interrupt
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fix: add style-src to CSP so inline styles in Help/Data panels render

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fix: reject oversized request bodies via Content-Length before parsing

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CHANGELOG update
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audit report files
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Quadratic blow-up in clustered layout DoS attack fixed, added MAX_ALL_PAIRS_MEMBERS and one virtual hub fallback option
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fix: bound token-session storage to stop disk-fill DoS (H2)

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fix: reject malformed TSV with 400 instead of crashing 500 (#1)

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fix: reject non-object session list members with 400 (#2)

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fix: sanitize edge weights to stop 500s and invalid-JSON output (#3, #4)

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fix: escapeHtml also escapes the single quote (#5)

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fix: escape channel color before interpolating into attribute value (#6)

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fix: URL-encode external session token in request path (#7)

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fix: rate-limit /api/ to blunt unauthenticated CPU-saturation (#8)

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lint / format backend
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Merge pull request #27 from Pavlopoulos-Lab/pre-release-security-auditing
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delete security audit reports
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cdd0440
fix: refresh node labels on predefined layout change

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style: restyle File panel action buttons with hierarchy and icons

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Commits on Jul 13, 2026

AGENTS.md with extra ruleset/guiderails
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