Up version, update docs

Makefile

@@ -7,8 +7,9 @@ BACKEND       := backend
 FRONTEND      := frontend
 PORT          ?= 3000
 DOCKER_USER   ?= xprilion
-VERSION       ?= 0.2.0
+VERSION       ?= 0.3.0
 DOCKER_COMPOSE := docker compose
+LOGO_SRC      := assets/full-logo.png
 
 # ─── Setup ────────────────────────────────────────────────
 
@@ -240,6 +241,40 @@ docs-docker: ## Run docs in Docker (port 4000)
 docs-build: ## Build docs to site/docs/.vitepress/dist
 	cd site && npx vitepress build docs
 
+# ─── Logo Generation ─────────────────────────────────────
+
+.PHONY: logo
+logo: ## Generate all logo sizes from assets/full-logo.png
+	@echo "Generating logo sizes from $(LOGO_SRC)..."
+	@mkdir -p $(FRONTEND)/public site/docs/public
+	@# Favicons for webapp
+	sips -z 16 16 $(LOGO_SRC) --out $(FRONTEND)/public/favicon-16x16.png
+	sips -z 32 32 $(LOGO_SRC) --out $(FRONTEND)/public/favicon-32x32.png
+	sips -z 180 180 $(LOGO_SRC) --out $(FRONTEND)/public/apple-touch-icon.png
+	sips -z 192 192 $(LOGO_SRC) --out $(FRONTEND)/public/logo-192.png
+	sips -z 512 512 $(LOGO_SRC) --out $(FRONTEND)/public/logo-512.png
+	@# Generate .ico from 32x32 (copy as favicon.ico for browsers)
+	cp $(FRONTEND)/public/favicon-32x32.png $(FRONTEND)/public/favicon.ico
+	@# Logo for header/nav
+	sips -z 64 64 $(LOGO_SRC) --out $(FRONTEND)/public/logo-64.png
+	@# OG image (1200x630 for social sharing - pad/crop as needed)
+	sips -z 630 630 $(LOGO_SRC) --out $(FRONTEND)/public/og-image-square.png
+	sips -p 630 1200 $(FRONTEND)/public/og-image-square.png --out $(FRONTEND)/public/og-image.png
+	rm $(FRONTEND)/public/og-image-square.png
+	@# Copy to docs site
+	cp $(FRONTEND)/public/favicon-16x16.png site/docs/public/
+	cp $(FRONTEND)/public/favicon-32x32.png site/docs/public/
+	cp $(FRONTEND)/public/favicon.ico site/docs/public/
+	cp $(FRONTEND)/public/apple-touch-icon.png site/docs/public/
+	cp $(FRONTEND)/public/logo-64.png site/docs/public/
+	cp $(FRONTEND)/public/logo-192.png site/docs/public/
+	cp $(FRONTEND)/public/logo-512.png site/docs/public/
+	cp $(FRONTEND)/public/og-image.png site/docs/public/
+	@# Full logo for README
+	cp $(LOGO_SRC) assets/logo.png
+	sips -z 200 200 $(LOGO_SRC) --out assets/logo-200.png
+	@echo "Done! Logo sizes generated in frontend/public/, site/docs/public/, and assets/"
+
 # ─── Cleanup ─────────────────────────────────────────────
 
 .PHONY: clean

README.md

@@ -1,6 +1,12 @@
-# OpenMLR
+<p align="center">
+  <img src="assets/logo-200.png" alt="OpenMLR Logo" width="120" />
+</p>
 
-A self-hosted ML research agent that plans, researches, writes papers, and executes code — all in one conversation.
+<h1 align="center">OpenMLR</h1>
+
+<p align="center">
+  A self-hosted ML research agent that plans, researches, writes papers, and executes code — all in one conversation.
+</p>
 
 [![Deploy to Render](https://render.com/images/deploy-to-render-button.svg)](https://render.com/deploy?repo=https://github.com/xprilion/OpenMLR)
 [![Deploy to Heroku](https://www.herokucdn.com/deploy/button.svg)](https://www.heroku.com/deploy?template=https://github.com/xprilion/OpenMLR)
@@ -16,6 +22,7 @@ A self-hosted ML research agent that plans, researches, writes papers, and execu
 - **Plan + Execute modes** — Plan mode gathers context; Execute mode does the work. Toggle with `Cmd+M`.
 - **Paper research** — OpenAlex, Semantic Scholar, arXiv, CrossRef, Papers With Code. Reads full papers, crawls citation graphs.
 - **Paper writing** — Section-by-section drafting with auto-save. Export to Markdown/LaTeX.
+- **Compute environments** — Execute code on local Docker, SSH remotes, or Modal cloud. Probe GPU/CPU capabilities.
 - **Background jobs** — Celery + Redis. Close the browser, come back later.
 - **Multi-provider LLMs** — OpenAI, Anthropic, OpenRouter, plus local models (Ollama, LM Studio).
 - **MCP servers** — Connect external tools via the Model Context Protocol.

backend/openmlr/app.py

@@ -19,7 +19,7 @@
 
 
 @asynccontextmanager
 async def lifespan(app: FastAPI):
     """Startup: create tables & shared state.  Shutdown: teardown sessions."""
     import logging
     logger = logging.getLogger("openmlr.app")
@@ -52,7 +52,7 @@
 app = FastAPI(
     title="OpenMLR",
     description="ML research intern — reads papers, trains models, writes papers",
-    version="2.0.0",
+    version="0.3.0",
     lifespan=lifespan,
 )
 
@@ -86,7 +86,7 @@
 
 # ── Global error handler ────────────────────────────────
 @app.exception_handler(Exception)
 async def global_exception_handler(request: Request, exc: Exception):
     import logging
     logger = logging.getLogger(__name__)
     logger.exception(f"Unhandled exception: {exc}")

backend/openmlr/routes/health.py

@@ -6,7 +6,7 @@
 
 router = APIRouter(tags=["health"])
 
-VERSION = "0.1.0"
+VERSION = "0.3.0"
 
 
 @router.get("/api/health")

backend/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "openmlr"
-version = "0.2.0"
+version = "0.3.0"
 description = "OpenMLR — an ML research intern that reads papers, trains models, and ships code"
 requires-python = ">=3.12"
 license = { text = "MIT" }

backend/tests/test_app.py

@@ -12,7 +12,7 @@ async def test_app_title(self):
         assert app.title == "OpenMLR"
 
     async def test_app_version(self):
-        assert app.version == "2.0.0"
+        assert app.version == "0.3.0"
 
     async def test_app_routers_registered(self):
         route_paths = [r.path for r in app.routes]

frontend/index.html

@@ -4,6 +4,31 @@
     <meta charset="UTF-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>OpenMLR</title>
+    <meta name="description" content="AI-powered ML Research Agent that plans tasks, researches papers, writes drafts, and executes code" />
+
+    <!-- Favicons -->
+    <link rel="icon" type="image/png" sizes="32x32" href="/favicon-32x32.png" />
+    <link rel="icon" type="image/png" sizes="16x16" href="/favicon-16x16.png" />
+    <link rel="apple-touch-icon" sizes="180x180" href="/apple-touch-icon.png" />
+    <link rel="icon" href="/favicon.ico" />
+
+    <!-- PWA -->
+    <link rel="manifest" href="/manifest.json" />
+    <meta name="theme-color" content="#3b82f6" />
+
+    <!-- Open Graph -->
+    <meta property="og:type" content="website" />
+    <meta property="og:title" content="OpenMLR - ML Research Agent" />
+    <meta property="og:description" content="AI-powered ML Research Agent that plans tasks, researches papers, writes drafts, and executes code" />
+    <meta property="og:image" content="/og-image.png" />
+    <meta property="og:url" content="https://openmlr.dev" />
+    <meta property="og:site_name" content="OpenMLR" />
+
+    <!-- Twitter Card -->
+    <meta name="twitter:card" content="summary_large_image" />
+    <meta name="twitter:title" content="OpenMLR - ML Research Agent" />
+    <meta name="twitter:description" content="AI-powered ML Research Agent that plans tasks, researches papers, writes drafts, and executes code" />
+    <meta name="twitter:image" content="/og-image.png" />
   </head>
   <body>
     <div id="root"></div>

frontend/public/manifest.json

@@ -0,0 +1,21 @@
+{
+  "name": "OpenMLR",
+  "short_name": "OpenMLR",
+  "description": "AI-powered ML Research Agent that plans tasks, researches papers, writes drafts, and executes code",
+  "start_url": "/",
+  "display": "standalone",
+  "background_color": "#0f172a",
+  "theme_color": "#3b82f6",
+  "icons": [
+    {
+      "src": "/logo-192.png",
+      "sizes": "192x192",
+      "type": "image/png"
+    },
+    {
+      "src": "/logo-512.png",
+      "sizes": "512x512",
+      "type": "image/png"
+    }
+  ]
+}

frontend/src/App.tsx

@@ -88,7 +88,7 @@
   const { uuid: routeUuid } = useParams<{ uuid: string }>();
 
   const [messages, setMessages] = useState<Message[]>([]);
   const [approvalEvent, setApprovalEvent] = useState<any>(null);
   const [conversations, setConversations] = useState<Conversation[]>([]);
   const [currentConvUuid, setCurrentConvUuid] = useState<string | null>(routeUuid || null);
   const [convStatuses, setConvStatuses] = useState<Record<string, ConvStatus>>({});
@@ -101,8 +101,8 @@
   const [viewingReport, setViewingReport] = useState<Resource | null>(null);
   const [inputMode, setInputMode] = useState<Mode>('plan');
   const [inputText, setInputText] = useState('');
   const [computeNodes, setComputeNodes] = useState<any[]>([]);
   const [activeCompute, setActiveCompute] = useState<any>(null);
 
   // Ref to always have current conv UUID in SSE callback (avoids stale closure)
   const currentConvUuidRef = useRef<string | null>(currentConvUuid);
@@ -172,14 +172,14 @@
       }
     };
     init();
   }, []);
 
   // Handle navigation to a different conversation via URL change
   useEffect(() => {
     if (routeUuid && routeUuid !== currentConvUuid) {
       switchConv(routeUuid);
     }
   }, [routeUuid]);
 
   const setCurrentConvStatus = useCallback((status: ConvStatus) => {
     setCurrentConvUuid((uuid) => {
@@ -199,8 +199,8 @@
       setApprovalEvent(null); setQuestionsPayload(null);
 
       // Load persisted tasks and resources from database
       setTasks(data.tasks?.map((t: any) => ({ title: t.title, status: t.status })) || []);
       setResources(data.resources?.map((r: any) => ({ 
         title: r.title, 
         url: r.url || '', 
         type: r.type,
@@ -212,7 +212,7 @@
         setRightPanelOpen(true);
       }
 
       setMessages(data.messages?.map((m: any) => {
         if (m.role === 'tool') {
           const meta = m.metadata || {};
           return { id: nextId(), role: 'tool' as const, content: '', metadata: { tool: meta.tool || 'tool', args: '', output: m.content, outputSuccess: meta.success !== false } };
@@ -276,7 +276,7 @@
     try {
       const data = await api.getConversation(uuid);
       if (data.messages) {
         setMessages(data.messages.map((m: any) => {
           if (m.role === 'tool') {
             const meta = m.metadata || {};
             return { id: nextId(), role: 'tool' as const, content: '', metadata: { tool: meta.tool || 'tool', args: '', output: m.content, outputSuccess: meta.success !== false } };
@@ -285,7 +285,7 @@
         }));
       }
       if (data.tasks?.length > 0 || data.resources?.length > 0) {
         setTasks(data.tasks?.map((t: any) => ({ title: t.title, status: t.status })) || []);
         setResources(data.resources?.map((r: any) => ({ title: r.title, url: r.url || '', type: r.type, id: r.id })) || []);
         setRightPanelOpen(true);
       }
@@ -555,6 +555,7 @@
       {/* Header */}
       <header className="flex items-center justify-between px-3 sm:px-6 h-14 bg-surface border-b border-border shrink-0 gap-2 sm:gap-4">
         <div className="flex items-center gap-2 sm:gap-3 shrink-0">
+          <img src="/logo-64.png" alt="OpenMLR" className="w-7 h-7 sm:w-8 sm:h-8" />
           <span className="font-bold text-base sm:text-lg text-primary tracking-tight">OpenMLR</span>
           <span 
             className={`w-2 h-2 rounded-full transition-colors duration-300 ${connected ? 'bg-success' : 'bg-error'}`} 

frontend/src/components/LoginPage.tsx

@@ -53,8 +53,11 @@ export function LoginPage({ onAuth }: Props) {
   return (
     <div className="min-h-screen bg-bg flex items-center justify-center p-6">
       <div className="w-full max-w-sm bg-surface rounded-2xl border border-border p-8 shadow-xl">
-        <h1 className="text-2xl font-bold text-primary text-center mb-1">OpenMLR</h1>
-        <p className="text-text-dim text-center mb-8">ML Research Intern</p>
+        <div className="flex flex-col items-center mb-6">
+          <img src="/logo-192.png" alt="OpenMLR" className="w-20 h-20 mb-3" />
+          <h1 className="text-2xl font-bold text-primary text-center">OpenMLR</h1>
+          <p className="text-text-dim text-center">ML Research Intern</p>
+        </div>
 
         {isFirstUser && (
           <div className="bg-primary/10 border border-primary/30 rounded-lg p-4 mb-6 text-sm text-text text-center">

site/docs/.vitepress/config.ts

@@ -10,9 +10,15 @@ export default defineConfig({
   cleanUrls: true,
 
   head: [
+    // Favicons
+    ["link", { rel: "icon", type: "image/png", sizes: "32x32", href: "/favicon-32x32.png" }],
+    ["link", { rel: "icon", type: "image/png", sizes: "16x16", href: "/favicon-16x16.png" }],
+    ["link", { rel: "apple-touch-icon", sizes: "180x180", href: "/apple-touch-icon.png" }],
+    ["link", { rel: "icon", href: "/favicon.ico" }],
+
     // Basic meta
     ["meta", { name: "author", content: "Anubhav Singh" }],
-    ["meta", { name: "theme-color", content: "#3eaf7c" }],
+    ["meta", { name: "theme-color", content: "#3b82f6" }],
     [
       "meta",
       {
@@ -48,6 +54,9 @@ export default defineConfig({
       },
     ],
     ["meta", { property: "og:url", content: "https://openmlr.dev" }],
+    ["meta", { property: "og:image", content: "https://openmlr.dev/og-image.png" }],
+    ["meta", { property: "og:image:width", content: "1200" }],
+    ["meta", { property: "og:image:height", content: "630" }],
 
     // Twitter Card
     ["meta", { name: "twitter:card", content: "summary_large_image" }],
@@ -60,6 +69,7 @@ export default defineConfig({
           "AI-powered ML Research Agent that plans tasks, researches papers, writes drafts, and executes code",
       },
     ],
+    ["meta", { name: "twitter:image", content: "https://openmlr.dev/og-image.png" }],
   ],
 
   // Sitemap generation
@@ -76,6 +86,7 @@ export default defineConfig({
       "configuration",
       "modes",
       "tools",
+      "compute",
       "architecture",
       "agent-harness",
       "api",
@@ -93,6 +104,7 @@ export default defineConfig({
   },
 
   themeConfig: {
+    logo: "/logo-64.png",
     nav: [
       { text: "Home", link: "/" },
       { text: "Setup", link: "/setup" },
@@ -113,6 +125,7 @@ export default defineConfig({
         items: [
           { text: "Modes (Plan / Execute)", link: "/modes" },
           { text: "Agent Tools", link: "/tools" },
+          { text: "Compute Environments", link: "/compute" },
         ],
       },
       {

site/docs/changelog.md

@@ -5,6 +5,35 @@ description: OpenMLR version history and release notes. Track new features, impr
 
 # Changelog
 
+## v0.3.0
+
+Compute environments, UI improvements, and bug fixes.
+
+### Compute Environments
+- **Multi-backend compute** — Execute code on local Docker, SSH remotes, or Modal cloud
+- **SSH key management** — Generate Ed25519/RSA keys, upload existing keys via Settings > Compute
+- **Compute probing** — Detect OS, GPUs (with CUDA version), Python versions, and disk space
+- **Compute selection** — Switch between configured compute nodes mid-conversation
+- **Connection pooling** — SSH connections are reused across tool calls for performance
+- **Docker-in-Docker detection** — Worker container executes commands directly when already in Docker
+
+### UI Improvements
+- **Collapsible Tasks & Resources** — Click section headers in the right panel to collapse/expand
+- **Fixed right panel layout** — Right panel no longer causes page scroll issues when toggled
+- **Improved scroll behavior** — Message list scrolls correctly without affecting page layout
+
+### Bug Fixes
+- Fixed `scrollIntoView` causing entire page to scroll when RightPanel is open
+- Fixed `_get_draft` database call using wrong function name
+- Fixed test suite failures related to async database mocking
+
+### Internal
+- Added `_running_in_container()` detection for Docker Compose worker environments
+- Improved test coverage for compute and writing tools
+- Updated Settings nav to reflect current menu structure
+
+---
+
 ## v0.2.0
 
 Major rewrite of the mode system, paper writing, processing architecture, and UI routing.