@seqyuan/annovibe 0.8.19 → 0.8.21

package/.next/server/app/page_client-reference-manifest.js

@@ -1 +1 @@
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package/.next/server/app-paths-manifest.json

@@ -18,26 +18,27 @@
   "/api/sessions/route": "app/api/sessions/route.js",
   "/api/soul/route": "app/api/soul/route.js",
   "/favicon.ico/route": "app/favicon.ico/route.js",
+  "/icon.svg/route": "app/icon.svg/route.js",
   "/api/agent/[id]/events/route": "app/api/agent/[id]/events/route.js",
-  "/api/auth/api-key/[provider]/route": "app/api/auth/api-key/[provider]/route.js",
   "/api/auth/all-providers/route": "app/api/auth/all-providers/route.js",
+  "/api/auth/api-key/[provider]/route": "app/api/auth/api-key/[provider]/route.js",
+  "/api/auth/login/[provider]/route": "app/api/auth/login/[provider]/route.js",
   "/api/auth/logout/[provider]/route": "app/api/auth/logout/[provider]/route.js",
   "/api/auth/providers/route": "app/api/auth/providers/route.js",
-  "/api/auth/login/[provider]/route": "app/api/auth/login/[provider]/route.js",
   "/api/internal/runtime/route": "app/api/internal/runtime/route.js",
   "/api/models-config/discover/route": "app/api/models-config/discover/route.js",
   "/api/models-config/route": "app/api/models-config/route.js",
-  "/api/models/route": "app/api/models/route.js",
   "/api/models-config/test/route": "app/api/models-config/test/route.js",
+  "/api/models/route": "app/api/models/route.js",
   "/api/plot-kernels/route": "app/api/plot-kernels/route.js",
   "/api/plot-kernels/status/route": "app/api/plot-kernels/status/route.js",
   "/api/plot-kernels/stop/route": "app/api/plot-kernels/stop/route.js",
-  "/api/settings/route": "app/api/settings/route.js",
+  "/api/reports/[id]/route": "app/api/reports/[id]/route.js",
   "/api/skills/install/route": "app/api/skills/install/route.js",
+  "/api/settings/route": "app/api/settings/route.js",
   "/api/skills/route": "app/api/skills/route.js",
-  "/api/version/route": "app/api/version/route.js",
   "/api/skills/search/route": "app/api/skills/search/route.js",
-  "/api/reports/[id]/route": "app/api/reports/[id]/route.js",
+  "/api/version/route": "app/api/version/route.js",
   "/login/page": "app/login/page.js",
   "/page": "app/page.js"
 }

package/.next/server/chunks/7601.js

@@ -124,15 +124,9 @@ Chat display rules:
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${b}`)}}destroy(){this._alive&&(this._alive=!1,this.idleTimer&&clearTimeout(this.idleTimer),this.unsubscribe?.(),this.onDestroyCallback?.())}preparePromptContext(a){this.applyRuntimePrompts(a)}async trackBusy(a,b){this.busyOperations.add(a),this.resetIdleTimer();try{return await b}finally{this.busyOperations.delete(a),this.resetIdleTimer()}}applyRuntimePrompts(a){if(!this.inner.agent.state||this.options.systemPromptDisabled)return;let b=(0,g.cV)(),c=this.inner.getActiveToolNames(),d=(0,l.R4)(c);if(!b.generativeUI){let a=(0,l.X8)((0,k.NP)((0,i.FE)(q(this.inner))));r(this.inner,s((0,k.zY)(a),d));return}let e=(0,l.X8)((0,k.NP)((0,i.FE)(q(this.inner)))),f=(0,i.zN)(e),h=(0,k.zY)(f),m=s(h,d),n=a?(0,j.WO)(m,a,{force:function(a){try{return a.getBranch().some(a=>!!a&&"object"==typeof a&&"message"===a.type&&!!a.message&&JSON.stringify(a.message).includes("show-widget"))}catch{return!1}}(this.inner.sessionManager)}):m;r(this.inner,n)}}function q(a){return"string"==typeof a._baseSystemPrompt?a._baseSystemPrompt:a.agent.state?.systemPrompt??""}function r(a,b){"string"==typeof a._baseSystemPrompt&&(a._baseSystemPrompt=b),a.agent.state&&(a.agent.state.systemPrompt=b)}function s(a,b){let c=(0,l.X8)(a);return b?(0,l.FJ)(c):c}function t(a){let b=(0,l.X8)((0,k.NP)((0,i.FE)(a.systemPrompt))),c=a.generativeUI?(0,k.zY)((0,i.zN)(b)):(0,k.zY)(b);return s(c,a.plotMode)}function u(){if(!globalThis.__piSessions){globalThis.__piSessions=new Map;let a=()=>globalThis.__piSessions?.forEach(a=>a.destroy());process.once("exit",a),process.once("SIGINT",a),process.once("SIGTERM",a)}return globalThis.__piSessions}function v(a){return u().get(a)}function w(){let a=[...u().values()].filter(a=>a.isAlive()).map(a=>a.getRuntimeStatus()),b=a.filter(a=>a.busy);return{busy:b.length>0,activeSessions:a.length,busySessions:b,sessions:a}}async function x(a,b,d,j){let k=u(),p=(globalThis.__piStartLocks||(globalThis.__piStartLocks=new 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+
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 AnnoVibe has a persistent Analysis Report tab. It is for curated analysis deliverables, not a transcript summary.
 
 When working on scientific or bioinformatics analysis, keep report-worthy content concise and structured:
@@ -140,6 +134,11 @@ When working on scientific or bioinformatics analysis, keep report-worthy conten
 - Do not include ordinary chat, reasoning traces, failed-debug logs, transient guesses, or results superseded by later parameter changes.
 - When an upstream input, threshold, parameter, or method changes, explicitly state which downstream results or interpretations are outdated and need refresh.
 - Prefer evidence-backed statements that cite generated files, tables, figures, scripts, or command outputs.
+- Make the report visually useful when figures exist: include 1-4 representative local image links with Markdown image syntax, for example \`![UMAP colored by cluster](results/umap_clusters.png)\`.
+- For each representative figure, add a one-sentence caption that states what the figure shows and why it matters biologically or analytically.
+- Put representative figures as a consecutive Markdown image block under a short heading so the Report tab can render them as a gallery: image line, then italic caption line, repeated.
+- Do not embed every generated image. Curate representative figures by topic, put the rest in the outputs table, and mention counts/directories.
+- Prefer browser-renderable figures in the report preview (PNG/JPG/SVG/HTML). If only PDFs exist, cite the PDF path and, when practical, create or mention a PNG preview.
 - If you ran tools for a bioinformatics/scientific analysis or created result directories, tables, figures, scripts, or reports, you MUST emit an analysis report update before finishing the response.
 - If the analysis produces many PDFs or figure files, do not expand them all in chat. Summarize them in the report by topic, output directory, counts, representative files, and the biological meaning of the figures.
 
@@ -165,6 +164,12 @@ When you have a compact report-worthy update, emit one or more fenced JSON block
 {"topic":"Short current analysis topic","section":"objective|input_data|methods|quality_control|results|interpretation|outputs|reproducibility","action":"append|replace","status":"draft|verified|needs_review|outdated","markdown":"Concise Markdown for the report section.","sources":["results/file.csv","HSPCs/"],"invalidates":["results"],"note":"Short change note."}
 \`\`\`
 
+Markdown quality requirements:
+- Use short paragraphs, compact tables, and local links to evidence files.
+- In \`results\`, lead with the main finding, then show representative figures and captions when available.
+- In \`outputs\`, group files by result type instead of listing a raw directory dump.
+- In \`interpretation\`, distinguish observed result, biological interpretation, and remaining uncertainty.
+
 Only use this fence for durable analysis summaries, not for chat narration or raw logs.
 </analysis-report-guidelines>`,e=/\n?\s*<analysis-report-guidelines>[\s\S]*?<\/analysis-report-guidelines>\s*/g;function f(a){return a.replace(e,"\n").replace(/\n{3,}/g,"\n\n").trim()}function g(a){return a.includes("<analysis-report-guidelines>")?a:a.trim()?`${a.trimEnd()}
 

package/.next/server/functions-config-manifest.json

@@ -5,8 +5,8 @@
       "runtime": "nodejs",
       "matchers": [
         {
-          "regexp": "^(?:\\/(_next\\/data\\/[^/]{1,}))?(?:\\/((?!_next\\/static|_next\\/image|favicon.ico|public).*))(\\.json)?[\\/#\\?]?$",
-          "originalSource": "/((?!_next/static|_next/image|favicon.ico|public).*)"
+          "regexp": "^(?:\\/(_next\\/data\\/[^/]{1,}))?(?:\\/((?!_next\\/static|_next\\/image|favicon.ico|icon.svg|public).*))(\\.json)?[\\/#\\?]?$",
+          "originalSource": "/((?!_next/static|_next/image|favicon.ico|icon.svg|public).*)"
         }
       ]
     },

package/.next/server/middleware-build-manifest.js

@@ -1 +1 @@
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+globalThis.__BUILD_MANIFEST={polyfillFiles:["static/chunks/polyfills-42372ed130431b0a.js"],devFiles:[],lowPriorityFiles:["static/cRtONXI0SmYC7X_hUWbB6/_buildManifest.js","static/cRtONXI0SmYC7X_hUWbB6/_ssgManifest.js"],rootMainFiles:["static/chunks/webpack-b0025b8b630debd5.js","static/chunks/4bd1b696-e356ca5ba0218e27.js","static/chunks/3794-123fdf632563f469.js","static/chunks/main-app-8d81a93b58bb990f.js"],rootMainFilesTree:{},pages:{"/_app":[]}};