scientify 2.1.0 → 3.1.0

package/README.en.md

@@ -226,8 +226,22 @@ Or invoke a specific skill directly with a slash command:
 /research-pipeline
 /research-collect
 /idea-generation
+/algorithm-selection
+/dataset-validate
 ```
 
+## New Skills for Midstream ML Work
+
+- `/algorithm-selection`
+  - use this after `/research-survey` and before `/research-plan`
+  - purpose: make 2-3 candidate routes explicit and record `Chosen Route / Rejected Routes / Fallback Route`
+- `/dataset-validate`
+  - use this when `plan_res.md` already exists and you want to validate data quality before implementation or model review
+  - purpose: review data reality, splits, labels, leakage risk, and mock-data usage separately from model quality
+- `/baseline-runner`
+  - use this when `plan_res.md` already exists and the project needs real baseline comparisons
+  - purpose: standardize baselines, protocol, metrics, and result recording, then write `baseline_res.md`
+
 ### 3. Monitor sub-agent progress
 
 When the orchestrator spawns sub-agents, you'll see:
@@ -262,11 +276,18 @@ Check status anytime:
 | **research-pipeline** | `/research-pipeline` | Orchestrator. Spawns sub-agents for each phase, verifies outputs between steps. |
 | **research-collect** | `/research-collect` | Search arXiv → filter → download .tex sources → cluster → generate survey report. |
 | **research-survey** | `/research-survey` | Deep analysis of papers: extract formulas, map to code, produce method comparison table. |
+| **algorithm-selection** | `/algorithm-selection` | Choose between 2-3 plausible ML routes, record rejected routes, and keep a fallback. |
 | **research-plan** | `/research-plan` | Create 4-part implementation plan (Dataset/Model/Training/Testing) from survey results. |
+| **dataset-validate** | `/dataset-validate` | Audit data reality, splits, labels, and leakage risk before model review. |
+| **baseline-runner** | `/baseline-runner` | Run or audit strong baselines under the same protocol before headline comparisons. |
 | **research-implement** | `/research-implement` | Implement ML code from plan, run 2-epoch validation with `uv` venv isolation. |
 | **research-review** | `/research-review` | Review implementation. Iterates fix → rerun → review up to 3 times. |
 | **research-experiment** | `/research-experiment` | Full training + ablation experiments. Requires review PASS. |
 | **idea-generation** | `/idea-generation` | Generate 5 innovative research ideas from a topic, select and enhance the best one. |
+| **write-paper** | `/write-paper` | Draft a result-driven paper or technical report from experiment artifacts. |
+| **artifact-review** | `/artifact-review` | Review a draft, README, or figure set before external sharing. |
+| **figure-standardize** | `/figure-standardize` | Normalize figure filenames, captions, labels, and reuse metadata. |
+| **release-layout** | `/release-layout` | Repackage existing artifacts into a clearer README or release entry surface. |
 
 </details>
 
@@ -306,7 +327,6 @@ Check status anytime:
 | `/papers` | List downloaded papers with metadata |
 | `/ideas` | List generated ideas |
 | `/projects` | List all projects |
-| `/project-switch <id>` | Switch active project |
 | `/project-delete <id>` | Delete a project |
 | `/research-subscribe ...` | Create/update scheduled Scientify jobs |
 | `/research-subscriptions` | Show your scheduled Scientify jobs |

package/README.md

@@ -226,8 +226,22 @@ openclaw gateway
 /research-pipeline
 /research-collect
 /idea-generation
+/algorithm-selection
+/dataset-validate
 ```
 
+## 机器学习中段任务的新增技能
+
+- `/algorithm-selection`
+  - 用在 `/research-survey` 之后、`/research-plan` 之前
+  - 作用：把 2-3 条候选路线写清楚，明确 `Chosen Route / Rejected Routes / Fallback Route`
+- `/dataset-validate`
+  - 用在 `plan_res.md` 已经存在、准备实现或审查模型之前
+  - 作用：单独审数据真实性、split、label、leakage 和 mock 风险，把数据质量和模型质量分开
+- `/baseline-runner`
+  - 用在 `plan_res.md` 已经存在、需要真实 baseline 对比时
+  - 作用：统一 baseline、协议、指标和结果记录，产出 `baseline_res.md`
+
 ### 3. 监控子 agent 进度
 
 编排器 spawn 子 agent 后，你会看到：
@@ -250,6 +264,19 @@ openclaw gateway
 /ideas                 # 列出已生成想法
 ```
 
+## 中后段项目的快捷技能
+
+如果项目已经有一部分产物，不必总是从 `/metabolism` 或 `/research-survey` 重新开始。可以直接进入这些 skill：
+
+- `/write-paper`
+  - 适合：已经有 `experiment_res.md`、结果图或结果表，准备整理成 paper draft
+- `/artifact-review`
+  - 适合：已有 draft、README 更新或准备对外分享的 figures，想先做发布前审查
+- `/figure-standardize`
+  - 适合：图已经有了，但文件名、caption、单位、标签风格不统一
+- `/release-layout`
+  - 适合：项目已有成果，想把 README 或 release 入口改得更清楚、更适合外部阅读
+
 ---
 
 ## 已知限制

package/dist/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../index.ts"],"names":[],"mappings":";;;;;;;AAiBA,wBA8EG"}

package/dist/index.js

@@ -1,55 +1,20 @@
 import path from "node:path";
 import { definePluginEntry } from "openclaw/plugin-sdk/plugin-entry";
 import { handleResearchStatus, handlePapers, handleIdeas, handleProjects, handleProjectSwitch, handleProjectDelete, } from "./src/commands.js";
-import { createResearchSubscribeHandler, createResearchSubscriptionsHandler, createResearchUnsubscribeHandler, } from "./src/research-subscriptions.js";
 import { createArxivSearchTool } from "./src/tools/arxiv-search.js";
-import { createArxivDownloadTool } from "./src/tools/arxiv-download.js";
-import { createGithubSearchTool } from "./src/tools/github-search-tool.js";
-import { createPaperBrowserTool } from "./src/tools/paper-browser.js";
 import { createOpenAlexSearchTool } from "./src/tools/openalex-search.js";
-import { createOpenReviewLookupTool } from "./src/tools/openreview-lookup.js";
-import { createUnpaywallDownloadTool } from "./src/tools/unpaywall-download.js";
-import { createScientifyCronTool } from "./src/tools/scientify-cron.js";
-import { createScientifyLiteratureStateTool } from "./src/tools/scientify-literature-state.js";
-import { createAutoUpdaterService } from "./src/services/auto-updater.js";
 import { createSkillInjectionHook } from "./src/hooks/inject-skill.js";
-import { createResearchModeHook } from "./src/hooks/research-mode.js";
-import { createScientifyCronAutofillHook } from "./src/hooks/scientify-cron-autofill.js";
-import { createScientifyMessageTrackerHook, createScientifySignaturePromptHook, createScientifyUsageCleanupHook, createScientifyUsageTrackerHook, } from "./src/hooks/scientify-signature.js";
 import { createCronSkillInjectionHook } from "./src/hooks/cron-skill-inject.js";
 import { registerResearchCli } from "./src/cli/research.js";
 import { handleMetabolismStatus } from "./src/commands/metabolism-status.js";
-// Default: check every hour
-const UPDATE_CHECK_INTERVAL_MS = 60 * 60 * 1000;
 export default definePluginEntry({
     id: "scientify",
     name: "Scientify",
-    description: "AI-powered research workflow automation with continuous knowledge metabolism",
+    description: "Continuous AI research workflow for survey, planning, implementation, review, experimentation, and writing",
     register(api) {
         // Register tools
         api.registerTool(createArxivSearchTool());
-        api.registerTool(createArxivDownloadTool());
-        api.registerTool(createGithubSearchTool());
-        api.registerTool(createPaperBrowserTool());
         api.registerTool(createOpenAlexSearchTool());
-        api.registerTool(createOpenReviewLookupTool());
-        api.registerTool(createUnpaywallDownloadTool());
-        api.registerTool(createScientifyCronTool({ runtime: api.runtime, logger: api.logger }));
-        api.registerTool(createScientifyLiteratureStateTool());
-        // Register auto-updater service (silent updates)
-        const pluginConfig = api.pluginConfig;
-        const autoUpdateEnabled = pluginConfig?.autoUpdate !== false; // enabled by default
-        if (autoUpdateEnabled) {
-            api.registerService(createAutoUpdaterService({
-                packageName: "scientify",
-                checkIntervalMs: UPDATE_CHECK_INTERVAL_MS,
-                logger: {
-                    info: (msg) => api.logger.info(msg),
-                    warn: (msg) => api.logger.warn(msg),
-                    debug: (msg) => api.logger.debug?.(msg),
-                },
-            }));
-        }
         // Register chat commands (bypass LLM)
         api.registerCommand({
             name: "research-status",
@@ -90,51 +55,11 @@ export default definePluginEntry({
             name: "project-delete",
             description: "Delete a research project (use --force to confirm)",
             acceptsArgs: true,
-            requireAuth: true, // Require auth for destructive operation
+            requireAuth: true,
             handler: handleProjectDelete,
         });
-        api.registerCommand({
-            name: "research-subscribe",
-            description: "Create/update a scheduled Scientify job (research digest or reminder). Example: /research-subscribe daily 09:00 Asia/Shanghai",
-            acceptsArgs: true,
-            requireAuth: false,
-            handler: createResearchSubscribeHandler({ runtime: api.runtime, logger: api.logger }),
-        });
-        api.registerCommand({
-            name: "research-subscriptions",
-            description: "Show your Scientify scheduled jobs",
-            acceptsArgs: false,
-            requireAuth: false,
-            handler: createResearchSubscriptionsHandler({ runtime: api.runtime, logger: api.logger }),
-        });
-        api.registerCommand({
-            name: "research-unsubscribe",
-            description: "Remove your Scientify scheduled jobs (or pass a specific job id)",
-            acceptsArgs: true,
-            requireAuth: false,
-            handler: createResearchUnsubscribeHandler({ runtime: api.runtime, logger: api.logger }),
-        });
         // Inject SKILL.md content into sessions_spawn tasks.
-        // Sub-agents run in "minimal" prompt mode and don't see <available_skills>,
-        // so this hook reads the matching SKILL.md and embeds it in the task body.
-        // api.source = entry file path (e.g. dist/index.js); findPluginRoot() walks
-        // up to locate openclaw.plugin.json, which is always at the plugin root.
         api.on("before_tool_call", createSkillInjectionHook(path.dirname(api.source)));
-        // Track whether a session actually used Scientify skills/tools.
-        // The signature is prompt-driven (model-generated), not post-processed.
-        api.on("before_tool_call", createScientifyUsageTrackerHook());
-        // Auto-fill cron delivery target from current conversation origin when omitted.
-        api.on("before_tool_call", createScientifyCronAutofillHook());
-        api.on("message_received", createScientifyMessageTrackerHook());
-        api.on("session_end", createScientifyUsageCleanupHook());
-        // Inject prompts at agent start so they affect the current turn.
-        // OpenClaw runs this hook before model execution and merges prependContext.
-        api.on("before_agent_start", createResearchModeHook(), {
-            priority: 100, // High priority to inject early
-        });
-        api.on("before_agent_start", createScientifySignaturePromptHook(), {
-            priority: 90,
-        });
         // Inject SKILL.md into cron session messages (for metabolism heartbeat).
         api.on("before_agent_start", createCronSkillInjectionHook());
         // Register CLI commands: openclaw research init/list/status/delete

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package/dist/src/cli/research.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"research.d.ts","sourceRoot":"","sources":["../../../src/cli/research.ts"],"names":[],"mappings":"AAiSA;;GAEG;AACH,wBAAgB,mBAAmB,CACjC,GAAG,EAAE,IAAI,CAAC,OAAO,aAAa,EAAE,iBAAiB,EAAE,aAAa,GAAG,QAAQ,CAAC,QA4D7E"}
+{"version":3,"file":"research.d.ts","sourceRoot":"","sources":["../../../src/cli/research.ts"],"names":[],"mappings":"AA6TA;;GAEG;AACH,wBAAgB,mBAAmB,CACjC,GAAG,EAAE,IAAI,CAAC,OAAO,aAAa,EAAE,iBAAiB,EAAE,aAAa,GAAG,QAAQ,CAAC,QA4D7E"}

package/dist/src/cli/research.js

@@ -2,6 +2,7 @@ import fs from "node:fs";
 import path from "node:path";
 import os from "node:os";
 import { renderBootstrapMd, renderSoulMd, renderAgentsMd } from "../templates/bootstrap.js";
+import { formatReleaseGateStatus, getReleaseGateNextStep, hasReleaseFacingArtifacts, readReleaseGateStatus } from "../release-gate.js";
 const OPENCLAW_HOME = path.join(os.homedir(), ".openclaw");
 const OPENCLAW_CONFIG = path.join(OPENCLAW_HOME, "openclaw.json");
 const CRON_JOBS_PATH = path.join(OPENCLAW_HOME, "cron", "jobs.json");
@@ -43,7 +44,7 @@ function addCronJob(agentId) {
         payload: {
             kind: "agentTurn",
             agentId,
-            message: "执行每日知识新陈代谢。阅读 AGENTS.md 了解工作流，然后使用 /metabolism 技能完成今日代谢。",
+            message: "Run daily knowledge metabolism. Read AGENTS.md for the workflow, then use the /metabolism skill to complete today's cycle.",
         },
         delivery: { mode: "announce" },
         enabled: true,
@@ -73,6 +74,20 @@ function findPluginSkillsDir(entryDir) {
     }
     return path.join(entryDir, "skills");
 }
+function copyDirectoryContents(src, dst) {
+    if (!fs.existsSync(src))
+        return;
+    fs.mkdirSync(dst, { recursive: true });
+    for (const entry of fs.readdirSync(src, { withFileTypes: true })) {
+        const srcPath = path.join(src, entry.name);
+        const dstPath = path.join(dst, entry.name);
+        if (entry.isDirectory()) {
+            copyDirectoryContents(srcPath, dstPath);
+            continue;
+        }
+        fs.copyFileSync(srcPath, dstPath);
+    }
+}
 function listResearchProjects() {
     const config = readOpenClawConfig();
     const agents = config.agents?.list ?? [];
@@ -86,7 +101,7 @@ function listResearchProjects() {
             : path.join(OPENCLAW_HOME, `workspace-${agent.id}`);
         let currentDay = 0;
         let createdAt = "";
-        const configPath = path.join(workspace, "metabolism", "config.json");
+        const configPath = path.join(workspace, "config.json");
         try {
             const mc = JSON.parse(fs.readFileSync(configPath, "utf-8"));
             currentDay = mc.currentDay ?? 0;
@@ -116,16 +131,18 @@ function initProject(id, pluginSkillsDir) {
     // 1. Create workspace directory structure
     const dirs = [
         workspace,
-        path.join(workspace, "metabolism"),
-        path.join(workspace, "metabolism", "knowledge"),
-        path.join(workspace, "metabolism", "diffs"),
-        path.join(workspace, "metabolism", "hypotheses"),
-        path.join(workspace, "metabolism", "log"),
-        path.join(workspace, "skills", "metabolism"),
-        path.join(workspace, "survey"),
         path.join(workspace, "papers"),
+        path.join(workspace, "knowledge"),
         path.join(workspace, "ideas"),
         path.join(workspace, "experiments"),
+        path.join(workspace, "paper"),
+        path.join(workspace, "paper", "sections"),
+        path.join(workspace, "paper", "figures"),
+        path.join(workspace, "paper", "build"),
+        path.join(workspace, "paper", "assets"),
+        path.join(workspace, "review"),
+        path.join(workspace, "log"),
+        path.join(workspace, "skills", "metabolism"),
     ];
     for (const dir of dirs) {
         fs.mkdirSync(dir, { recursive: true });
@@ -143,6 +160,15 @@ function initProject(id, pluginSkillsDir) {
     else {
         console.warn(`Warning: metabolism SKILL.md not found at ${srcSkill}`);
     }
+    // 3b. Copy paper starter bundle from write-paper references
+    const srcLatexBundle = path.join(pluginSkillsDir, "write-paper", "references", "latex");
+    const dstPaperDir = path.join(workspace, "paper");
+    if (fs.existsSync(srcLatexBundle)) {
+        copyDirectoryContents(srcLatexBundle, dstPaperDir);
+    }
+    else {
+        console.warn(`Warning: LaTeX starter bundle not found at ${srcLatexBundle}`);
+    }
     // 4. Modify openclaw.json
     const config = readOpenClawConfig();
     // Add agent to agents.list
@@ -179,12 +205,10 @@ function showStatus(id) {
         console.error(`Error: research project '${id}' not found`);
         process.exit(1);
     }
-    const knowledgeDir = path.join(project.workspace, "metabolism", "knowledge");
-    const hypothesesDir = path.join(project.workspace, "metabolism", "hypotheses");
-    const diffsDir = path.join(project.workspace, "metabolism", "diffs");
+    const knowledgeDir = path.join(project.workspace, "knowledge");
+    const hypothesesDir = path.join(project.workspace, "ideas");
     let topicCount = 0;
     let hypothesisCount = 0;
-    let latestDiffs = [];
     try {
         topicCount = fs.readdirSync(knowledgeDir).filter((f) => f.startsWith("topic-")).length;
     }
@@ -193,22 +217,22 @@ function showStatus(id) {
         hypothesisCount = fs.readdirSync(hypothesesDir).filter((f) => f.endsWith(".md")).length;
     }
     catch { /* empty */ }
-    try {
-        latestDiffs = fs
-            .readdirSync(diffsDir)
-            .filter((f) => f.endsWith(".md"))
-            .sort()
-            .slice(-3);
-    }
-    catch { /* empty */ }
     console.log(`\nResearch Project: ${id}`);
     console.log(`  Agent:      ${project.agentId}`);
     console.log(`  Workspace:  ${project.workspace}`);
     console.log(`  Day:        ${project.currentDay}`);
     console.log(`  Topics:     ${topicCount}`);
     console.log(`  Hypotheses: ${hypothesisCount}`);
-    if (latestDiffs.length > 0) {
-        console.log(`  Recent diffs: ${latestDiffs.join(", ")}`);
+    const gateStatus = readReleaseGateStatus(project.workspace);
+    if (hasReleaseFacingArtifacts(project.workspace) || gateStatus.state !== "missing") {
+        console.log(`  Release:    ${formatReleaseGateStatus(gateStatus)}`);
+        if (gateStatus.state === "stale" && gateStatus.staleReasons.length > 0) {
+            console.log(`  Gate Note:  ${gateStatus.staleReasons[0]}`);
+        }
+        const nextStep = getReleaseGateNextStep(project.workspace, gateStatus);
+        if (nextStep) {
+            console.log(`  Next:       ${nextStep}`);
+        }
     }
     if (project.createdAt) {
         console.log(`  Created:    ${project.createdAt}`);

package/dist/src/cli/research.js.map

@@ -1 +1 @@
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package/dist/src/commands/metabolism-status.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"metabolism-status.d.ts","sourceRoot":"","sources":["../../../src/commands/metabolism-status.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,oBAAoB,EAAE,mBAAmB,EAAE,MAAM,aAAa,CAAC;AA6E7E;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CA0CtF"}
+{"version":3,"file":"metabolism-status.d.ts","sourceRoot":"","sources":["../../../src/commands/metabolism-status.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,oBAAoB,EAAE,mBAAmB,EAAE,MAAM,aAAa,CAAC;AAiE7E;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CAiCtF"}

package/dist/src/commands/metabolism-status.js

@@ -19,10 +19,10 @@ function findProjectWorkspace() {
     }
     const agents = config.agents?.list ?? [];
     const researchAgents = agents.filter((a) => a.id.startsWith("research-"));
-    // Try each research agent workspace to find one with metabolism/config.json
+    // Try each research agent workspace to find one with config.json
     for (const agent of researchAgents) {
         const workspace = (agent.workspace ?? `~/.openclaw/workspace-${agent.id}`).replace("~", os.homedir());
-        const metabolismConfig = path.join(workspace, "metabolism", "config.json");
+        const metabolismConfig = path.join(workspace, "config.json");
         if (fs.existsSync(metabolismConfig)) {
             return { workspace, projectId: agent.id.replace("research-", "") };
         }
@@ -37,7 +37,7 @@ function findProjectWorkspace() {
 }
 function readMetabolismConfig(workspace) {
     try {
-        return JSON.parse(fs.readFileSync(path.join(workspace, "metabolism", "config.json"), "utf-8"));
+        return JSON.parse(fs.readFileSync(path.join(workspace, "config.json"), "utf-8"));
     }
     catch {
         return null;
@@ -52,19 +52,6 @@ function countFiles(dirPath, filter) {
         return 0;
     }
 }
-function readRecentDiffs(workspace, count) {
-    const diffsDir = path.join(workspace, "metabolism", "diffs");
-    try {
-        return fs
-            .readdirSync(diffsDir)
-            .filter((f) => f.endsWith(".md"))
-            .sort()
-            .slice(-count);
-    }
-    catch {
-        return [];
-    }
-}
 /**
  * /metabolism-status — Show knowledge metabolism status
  */
@@ -75,9 +62,8 @@ export function handleMetabolismStatus(_ctx) {
     }
     const { workspace, projectId } = project;
     const config = readMetabolismConfig(workspace);
-    const topicCount = countFiles(path.join(workspace, "metabolism", "knowledge"), (f) => f.startsWith("topic-"));
-    const hypothesisCount = countFiles(path.join(workspace, "metabolism", "hypotheses"), (f) => f.endsWith(".md"));
-    const recentDiffs = readRecentDiffs(workspace, 3);
+    const topicCount = countFiles(path.join(workspace, "knowledge"), (f) => f.startsWith("topic-"));
+    const hypothesisCount = countFiles(path.join(workspace, "ideas"), (f) => f.endsWith(".md"));
     let output = `**Metabolism Status — ${projectId}**\n\n`;
     if (!config) {
         output += "Status: Pending BOOTSTRAP configuration\n";
@@ -89,12 +75,6 @@ export function handleMetabolismStatus(_ctx) {
     output += `Topics: ${topicCount}\n`;
     output += `Hypotheses: ${hypothesisCount}\n`;
     output += `Heartbeat: ${heartbeatStatus}\n`;
-    if (recentDiffs.length > 0) {
-        output += `\nRecent diffs:\n`;
-        for (const diff of recentDiffs) {
-            output += `  ${diff}\n`;
-        }
-    }
     return { text: output };
 }
 //# sourceMappingURL=metabolism-status.js.map

package/dist/src/commands/metabolism-status.js.map

@@ -1 +1 @@
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package/dist/src/commands.d.ts

@@ -1,26 +1,26 @@
 import type { PluginCommandContext, PluginCommandResult } from "./types.js";
 /**
- * /research-status - Show workspace status
+ * /research-status - Show workspace status for all research agents
  */
 export declare function handleResearchStatus(_ctx: PluginCommandContext): PluginCommandResult;
 /**
- * /papers - List downloaded papers
+ * /papers - List downloaded papers in a research agent workspace
  */
 export declare function handlePapers(ctx: PluginCommandContext): PluginCommandResult;
 /**
- * /ideas - List generated ideas
+ * /ideas - List generated ideas in a research agent workspace
  */
 export declare function handleIdeas(ctx: PluginCommandContext): PluginCommandResult;
 /**
- * /projects - List all research projects
+ * /projects - List all research projects (alias for /research-status)
  */
 export declare function handleProjects(_ctx: PluginCommandContext): PluginCommandResult;
 /**
- * /project-switch <project-id> - Switch to a different project
+ * /project-switch - No longer needed (each agent has its own workspace)
  */
-export declare function handleProjectSwitch(ctx: PluginCommandContext): PluginCommandResult;
+export declare function handleProjectSwitch(_ctx: PluginCommandContext): PluginCommandResult;
 /**
- * /project-delete <project-id> - Delete a research project
+ * /project-delete - Delete via CLI instead
  */
-export declare function handleProjectDelete(ctx: PluginCommandContext): PluginCommandResult;
+export declare function handleProjectDelete(_ctx: PluginCommandContext): PluginCommandResult;
 //# sourceMappingURL=commands.d.ts.map

package/dist/src/commands.d.ts.map

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