@seqyuan/annovibe 0.8.83 → 0.8.85

package/.next/server/chunks/6429.js

@@ -137,14 +137,14 @@ if (window.Chart) init();
 ${h.content}
 </widget-guidelines>`;return g?`${g}
 
-${j}`:j}},39737:(a,b,c)=>{"use strict";c.d(b,{L:()=>o});var d=c(29021),e=c(33873),f=c(23537);let g=["read","bash","grep","find","ls"],h=["read","bash","edit","write","grep","find","ls"],i=[/\brm\b/i,/\brmdir\b/i,/\bmv\b/i,/\bcp\b/i,/\bmkdir\b/i,/\btouch\b/i,/\bchmod\b/i,/\bchown\b/i,/\bchgrp\b/i,/\bln\b/i,/\btee\b/i,/\btruncate\b/i,/\bdd\b/i,/\bshred\b/i,/[^<]>(?!>)/,/>>/,/\bnpm\s+(install|uninstall|update|ci|link|publish)/i,/\byarn\s+(add|remove|install|publish)/i,/\bpnpm\s+(add|remove|install|publish)/i,/\bpip\s+(install|uninstall)/i,/\bapt(?:-get)?\s+(install|remove|purge|update|upgrade)/i,/\bbrew\s+(install|uninstall|upgrade)/i,/\bgit\s+(add|commit|push|pull|merge|rebase|reset|checkout\s+-b|branch\s+-[dD]|stash|cherry-pick|revert|tag|init|clone)/i,/\bsudo\b/i,/\bsu\b/i,/\bkill\b/i,/\bpkill\b/i,/\bkillall\b/i,/\breboot\b/i,/\bshutdown\b/i,/\bsystemctl\s+(start|stop|restart|enable|disable)/i,/\bservice\s+\S+\s+(start|stop|restart)/i,/\b(vim?|nano|emacs|code|subl)\b/i],j=[/^\s*cat\b/,/^\s*head\b/,/^\s*tail\b/,/^\s*less\b/,/^\s*more\b/,/^\s*grep\b/,/^\s*find\b/,/^\s*ls\b/,/^\s*pwd\b/,/^\s*echo\b/,/^\s*printf\b/,/^\s*wc\b/,/^\s*sort\b/,/^\s*uniq\b/,/^\s*diff\b/,/^\s*file\b/,/^\s*stat\b/,/^\s*du\b/,/^\s*df\b/,/^\s*tree\b/,/^\s*which\b/,/^\s*whereis\b/,/^\s*type\b/,/^\s*env\b/,/^\s*printenv\b/,/^\s*uname\b/,/^\s*whoami\b/,/^\s*id\b/,/^\s*date\b/,/^\s*cal\b/,/^\s*uptime\b/,/^\s*ps\b/,/^\s*top\b/,/^\s*htop\b/,/^\s*free\b/,/^\s*git\s+(status|log|diff|show|branch|remote|config\s+--get)/i,/^\s*git\s+ls-/i,/^\s*npm\s+(list|ls|view|info|search|outdated|audit)/i,/^\s*yarn\s+(list|info|why|audit)/i,/^\s*node\s+--version/i,/^\s*python\s+--version/i,/^\s*curl\s/i,/^\s*wget\s+-O\s*-/i,/^\s*jq\b/,/^\s*sed\s+-n/i,/^\s*awk\b/,/^\s*rg\b/,/^\s*fd\b/,/^\s*bat\b/,/^\s*exa\b/,/^\s*R\s+-e/i,/^\s*Rscript\s+-e/i],k=".annovibe-plan.md";function l(a){return(0,e.join)(a,k)}function m(a,b,c){let e=c.length>0?["","## Steps","",...c.map(a=>`${a.completed?"- [x]":"- [ ]"} ${a.text}`)].join("\n"):"";(0,d.writeFileSync)(l(a),`# Annovibe Plan
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 This plan was generated by the Annovibe AI agent.
 It is read-only until the plan is approved for execution.
 
 ${b}${e}
-`)}function n(a){try{(0,d.unlinkSync)(l(a))}catch{}}function o(a){let b=!1,c=!1,e=!1,o=[];function p(a){a!==b&&(b=a,a||(e=!1,o=[]))}function q(b){let c=b?(0,f.xt)(b):void 0;if(c)return void p(c.enabled);let d=a.getActiveTools();p(d.length>0&&d.every(a=>g.includes(a))&&!d.includes("edit")&&!d.includes("write"))}async function r(c){let d=c.sessionManager.getSessionId();b=!b,(0,f.hv)(d,b),e=!1,o=[],b?(await a.setActiveTools(g),c.ui.notify(`Plan mode enabled. Tools: ${g.join(", ")}`)):(await a.setActiveTools(h),c.ui.notify("Plan mode disabled. Full access restored."))}a.registerCommand("plan",{description:"Toggle plan mode (read-only exploration)",handler:async(a,b)=>{await r(b)}}),a.registerFlag("plan",{description:"Start in plan mode (read-only exploration)",type:"boolean",default:!1}),a.on("tool_call",async(a,c)=>{if(q(c.sessionManager.getSessionId()),!b||"bash"!==a.toolName)return;let d=a.input.command;if((!j.some(a=>a.test(d))||i.some(a=>a.test(d)))&&i.some(a=>a.test(d)))return{block:!0,reason:`Plan mode: destructive command blocked. Use /plan to disable plan mode first.
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+`)}function o(a){try{(0,d.unlinkSync)(m(a))}catch{}}function p(a){let b=!1,c=!1,e=!1,p=[],q=null;function r(){return{enabled:b,todos:p.map(a=>({step:a.step,text:a.text,completed:a.completed})),executing:e}}function s(){let b=r();q&&(0,g.qX)(q,b)||(a.appendEntry("plan-mode",b),q=b)}function t(a){a!==b&&(b=a,a||(e=!1,p=[]))}function u(b){let c=b?(0,f.xt)(b):void 0;if(c)return void t(c.enabled);let d=a.getActiveTools();t(d.length>0&&d.every(a=>h.includes(a))&&!d.includes("edit")&&!d.includes("write"))}async function v(c){let d=c.sessionManager.getSessionId();b=!b,(0,f.hv)(d,b),e=!1,p=[],b?(await a.setActiveTools(h),c.ui.notify(`Plan mode enabled. Tools: ${h.join(", ")}`)):(await a.setActiveTools(i),c.ui.notify("Plan mode disabled. Full access restored."))}a.registerCommand("plan",{description:"Toggle plan mode (read-only exploration)",handler:async(a,b)=>{await v(b)}}),a.registerFlag("plan",{description:"Start in plan mode (read-only exploration)",type:"boolean",default:!1}),a.on("tool_call",async(a,c)=>{if(u(c.sessionManager.getSessionId()),!b||"bash"!==a.toolName)return;let d=a.input.command;if((!k.some(a=>a.test(d))||j.some(a=>a.test(d)))&&j.some(a=>a.test(d)))return{block:!0,reason:`Plan mode: destructive command blocked. Use /plan to disable plan mode first.
+Command: ${d}`}}),a.on("tool_result",async(a,b)=>{if(c=!0,!e||0===p.length)return;let d=p.find(a=>!a.completed);d&&(d.completed=!0,s())}),a.on("context",async(a,c)=>{if(u(c.sessionManager.getSessionId()),!b)return{messages:a.messages.filter(a=>!("user"===a.role&&Array.isArray(a.content)&&a.content.some(a=>"text"===a.type&&a.text?.includes("[PLAN MODE ACTIVE]")))&&!0)}}),a.on("before_agent_start",async(a,c)=>{if(u(c.sessionManager.getSessionId()),b||e){if(b)return{message:{customType:"plan-mode-context",content:`[PLAN MODE ACTIVE]
 You are in plan mode — a read-only exploration mode for safe code analysis.
 
 Restrictions:
@@ -158,28 +158,28 @@ Create a detailed numbered plan:
 2. Second step description
 ...
 
-Do NOT make changes — just describe what you would do.`,display:!1}};if(e&&o.length>0){let a=o.filter(a=>!a.completed);return{message:{customType:"plan-execution-context",content:`[EXECUTING PLAN — Full tool access enabled]
+Do NOT make changes — just describe what you would do.`,display:!1}};if(e&&p.length>0){let a=p.filter(a=>!a.completed);return{message:{customType:"plan-execution-context",content:`[EXECUTING PLAN — Full tool access enabled]
 
 Remaining steps:
 ${a.map(a=>`${a.step}. ${a.text}`).join("\n")}
 
-Execute each step in order.`,display:!1}}}}}),a.on("agent_end",async(c,d)=>{if(q(d.sessionManager.getSessionId()),e&&o.length>0){o.every(a=>a.completed)&&(a.sendMessage({customType:"plan-complete",content:`**Plan Complete!** ✓
+Execute each step in order.`,display:!1}}}}}),a.on("agent_end",async(c,d)=>{if(u(d.sessionManager.getSessionId()),e&&p.length>0){p.every(a=>a.completed)&&(a.sendMessage({customType:"plan-complete",content:`**Plan Complete!** ✓
 
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 Saved plan:
 
 ${b}
 
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Use it for reproducible R/Python analysis plots, data visualizations, and warm-runtime analysis work.\n\nTool routing:\n- Use `kernel_plot_render` for one-shot iterative plot previews — images auto-render inline in chat without saving files. Call `render_plot()` to mark the preview target. ggplot2 (R) and plt.show() (Python) are auto-captured as convenience.\n- Use `kernel_plot_inspect` after resuming a workbench session, after suspected kernel restart, or whenever you are unsure whether objects like `adata`/`seurat_obj` are still live in memory.\n- Use `kernel_plot_run` when plots depend on data already loaded in warm kernel memory, or when saving final artifacts to disk.\n- Use `runtime: \"kernel-lite\"` in `kernel_plot_run` when variables or loaded data should persist across turns.\n- Use `runtime: \"worker\"` for one-shot scripts that should be isolated.\n- Do not run Rscript/python plotting through `bash` unless the workbench tools are unavailable.\n- Do not use bash with `conda run python`, `Rscript`, or direct interpreter calls for analysis code — always prefer `kernel_plot_run`.\n\nkernel-lite memory rules — CRITICAL:\n- Packages imported (import scanpy, library(Seurat), etc.) and variables assigned in one kernel_plot_run call persist while the same kernel-lite runtime is alive. Do NOT repeat imports in every call. Import each package only once, in the first call that needs it.\n- Large data objects loaded via sc.read(), readRDS(), qread(), pd.read_csv(), etc. stay in memory while the warm kernel is alive. Before calling any load function, check whether the object already exists:\n  Python: `if 'adata' not in globals(): adata = sc.read(path)`\n  R: `if (!exists('seurat_obj')) seurat_obj <- readRDS(path)`\n  Print a brief note when reusing in-memory data vs loading fresh.\n- Do NOT put sc.read() / readRDS() / qread() at the top of every call. This reloads multi-GB files needlessly and is the #1 performance mistake in workbench sessions.\n- After browser refreshes, model switches, compaction, or a resumed workbench session, treat prior history as inferred only: first use `kernel_plot_inspect` or an explicit existence check to see whether required objects still exist, then reload only missing objects from the known source path.\n\nWorkbench artifact rules:\n- Save every output under `WARMPLOT_OUTPUT_DIR` or `PI_KERNEL_PLOT_OUTPUT_DIR`.\n- Create a primary PNG/JPEG/WebP preview for chat display whenever a figure is produced, not PDF-only output. Keep the preview reasonably sized so it can be embedded inline.\n- If a publication-quality PDF/SVG is needed, save it in addition to the preview image.\n- Name the primary preview clearly, for example `00_preview.png`, so it is easy to identify.\n- When the user asks to save final outputs to a specific project directory, use that directory (not WARMPLOT_OUTPUT_DIR) for the final artifacts.\n\nChat display rules:\n- The web chat renders returned image artifacts inline. Do not say that images cannot be displayed.\n- Do not use `open`, `xdg-open`, or desktop viewers to show plots.\n- After generating any plot, make the chat response displayable by including the PNG/JPEG/WebP preview path in the final answer or by returning it as a tool image artifact. Do not mention only PDF paths when an image preview exists.\n- When using shell tools for plotting, still save a PNG/JPEG/WebP preview and include that preview path in the final answer; avoid a final answer that only says a desktop window was opened.\n- When the user asks to show an existing PNG/JPEG/WebP file, use `read` on that image path; the UI will display the image even if the model cannot inspect pixels.\n- If only a PDF exists and the user asks to see it in chat, generate a PNG preview with `kernel_plot_run` or report the PDF path only if conversion is not practical.\n- After a successful plot, summarize the result briefly and include both preview image paths and any publication-quality PDF/SVG paths.\n</workbench-guidelines>",e=/\n?\s*(?:<plot-mode-guidelines>[\s\S]*?<\/plot-mode-guidelines>|<workbench-guidelines>[\s\S]*?<\/workbench-guidelines>)\s*/g;function f(a){return a.replace(e,"\n").replace(/\n{3,}/g,"\n\n").trim()}function g(a){return a.includes("<plot-mode-guidelines>")||a.includes("<workbench-guidelines>")?a:a.trim()?`${a.trimEnd()}
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 ${d}
 ## WeCom IM Channel Constraints
@@ -193,7 +193,7 @@ You are responding to a user via 企业微信 (WeCom) bot. Follow these rules:
 5. **Respond in the user's language.** If the user sends Chinese, reply in Chinese.
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package/.next/server/chunks/7914.js

@@ -1,6 +1,6 @@
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package/.next/server/pages/404.html

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package/.next/server/server-reference-manifest.json

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