scientify 3.0.0 → 3.2.0

package/README.en.md

@@ -172,13 +172,11 @@ After `openclaw gateway`, the WebUI is available at **http://127.0.0.1:18789/**
 
 ## Install Scientify
 
-### From npm (recommended)
-
 ```bash
-openclaw plugins install scientify
+openclaw plugins install "$(npm pack scientify)"
 ```
 
-The plugin installs to `~/.openclaw/extensions/scientify/` and is automatically enabled.
+The plugin installs to `~/.openclaw/extensions/` and is automatically enabled.
 
 ### From source (development)
 
@@ -194,7 +192,7 @@ openclaw plugins install -l ./
 
 ```bash
 openclaw plugins list
-# Should show: scientify (enabled)
+# Should show: Scientify (loaded)
 ```
 
 After installation, **restart the gateway** to load the plugin:
@@ -226,8 +224,22 @@ 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 +274,18 @@ 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 +325,6 @@ 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

@@ -172,18 +172,16 @@ openclaw gateway
 
 ## 安装 Scientify
 
-### 从 npm 安装（推荐）
-
 ```bash
-openclaw plugins install scientify
+openclaw plugins install "$(npm pack scientify)"
 ```
 
-插件安装到 `~/.openclaw/extensions/scientify/`，自动启用。
+插件安装到 `~/.openclaw/extensions/`，自动启用。
 
 ### 从源码安装（开发用）
 
 ```bash
-git clone https://github.com/user/scientify.git
+git clone https://github.com/tsingyuai/scientify.git
 cd scientify && pnpm install && pnpm build
 
 # 链接为开发插件
@@ -194,7 +192,7 @@ openclaw plugins install -l ./
 
 ```bash
 openclaw plugins list
-# 应显示: scientify (enabled)
+# 应显示: Scientify (loaded)
 ```
 
 安装后需 **重启 Gateway** 以加载插件：
@@ -226,8 +224,22 @@ 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 +262,19 @@ 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.js

@@ -8,9 +8,9 @@ import { createCronSkillInjectionHook } from "./src/hooks/cron-skill-inject.js";
 import { registerResearchCli } from "./src/cli/research.js";
 import { handleMetabolismStatus } from "./src/commands/metabolism-status.js";
 export default definePluginEntry({
-    id: "scientify",
+    id: "scientify-tsingyuai",
     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());

package/dist/index.js.map

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

@@ -1 +1 @@
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+{"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 ?? [];
@@ -120,6 +135,12 @@ function initProject(id, pluginSkillsDir) {
         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"),
     ];
@@ -139,6 +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
@@ -193,6 +223,17 @@ function showStatus(id) {
     console.log(`  Day:        ${project.currentDay}`);
     console.log(`  Topics:     ${topicCount}`);
     console.log(`  Hypotheses: ${hypothesisCount}`);
+    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.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"commands.d.ts","sourceRoot":"","sources":["../../src/commands.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,oBAAoB,EAAE,mBAAmB,EAAE,MAAM,YAAY,CAAC;AAqC5E;;GAEG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CA8BpF;AAED;;GAEG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CA+B3E;AAED;;GAEG;AACH,wBAAgB,WAAW,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CA4B1E;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CAE9E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CAEnF;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CAEnF"}
+{"version":3,"file":"commands.d.ts","sourceRoot":"","sources":["../../src/commands.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,oBAAoB,EAAE,mBAAmB,EAAE,MAAM,YAAY,CAAC;AAgN5E;;GAEG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CAiDpF;AAED;;GAEG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CA+B3E;AAED;;GAEG;AACH,wBAAgB,WAAW,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CA4B1E;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CAE9E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CAEnF;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CAEnF"}

package/dist/src/commands.js

@@ -1,6 +1,7 @@
 import * as fs from "node:fs";
 import * as path from "node:path";
 import * as os from "node:os";
+import { formatReleaseGateStatus, getReleaseGateNextStep, hasReleaseFacingArtifacts, readReleaseGateStatus } from "./release-gate.js";
 const OPENCLAW_HOME = path.join(os.homedir(), ".openclaw");
 /**
  * List all research agents from openclaw.json.
@@ -30,6 +31,144 @@ function countFiles(dirPath, filter) {
         return 0;
     }
 }
+function fileExists(filePath) {
+    try {
+        return fs.existsSync(filePath);
+    }
+    catch {
+        return false;
+    }
+}
+function readLatestReviewVerdict(workspace) {
+    const iterationsDir = path.join(workspace, "iterations");
+    if (!fileExists(iterationsDir))
+        return "MISSING";
+    try {
+        const files = fs.readdirSync(iterationsDir)
+            .filter((f) => /^judge_v\d+\.md$/.test(f))
+            .sort((a, b) => {
+            const na = Number(a.match(/\d+/)?.[0] ?? "0");
+            const nb = Number(b.match(/\d+/)?.[0] ?? "0");
+            return nb - na;
+        });
+        const latest = files[0];
+        if (!latest)
+            return "MISSING";
+        const content = fs.readFileSync(path.join(iterationsDir, latest), "utf-8");
+        const verdictMatch = content.match(/##\s+Verdict:\s+([A-Z_]+)/);
+        const verdict = verdictMatch?.[1];
+        return verdict ?? "UNKNOWN";
+    }
+    catch {
+        return "UNKNOWN";
+    }
+}
+function buildProjectSnapshot(workspace) {
+    return {
+        hasConfig: fileExists(path.join(workspace, "config.json")),
+        hasSurvey: fileExists(path.join(workspace, "survey_res.md")),
+        hasSelection: fileExists(path.join(workspace, "selection_res.md")),
+        hasPlan: fileExists(path.join(workspace, "plan_res.md")),
+        hasDataValidation: fileExists(path.join(workspace, "data_validation.md")),
+        hasBaseline: fileExists(path.join(workspace, "baseline_res.md")),
+        hasImplementationReport: fileExists(path.join(workspace, "ml_res.md")),
+        latestReviewVerdict: readLatestReviewVerdict(workspace),
+        hasExperiment: fileExists(path.join(workspace, "experiment_res.md")),
+    };
+}
+function inferNextAction(snapshot) {
+    if (!snapshot.hasConfig) {
+        return {
+            stage: "Bootstrap pending",
+            command: "complete BOOTSTRAP configuration",
+            expectedOutputs: ["config.json", "SOUL.md"],
+            reason: "The project is missing its base configuration, so later survey, selection, and experiment steps do not yet share a stable direction.",
+        };
+    }
+    if (!snapshot.hasSurvey) {
+        return {
+            stage: "Survey needed",
+            command: "/research-survey",
+            expectedOutputs: ["knowledge/", "survey_res.md"],
+            reason: "There is no deep survey result yet, so route selection and implementation would be premature.",
+        };
+    }
+    if (!snapshot.hasSelection && !snapshot.hasPlan) {
+        return {
+            stage: "Route selection",
+            command: "/algorithm-selection",
+            expectedOutputs: ["selection_res.md"],
+            reason: "A survey exists, but the project has not yet narrowed candidate approaches into Chosen / Rejected / Fallback routes.",
+        };
+    }
+    if (!snapshot.hasPlan) {
+        return {
+            stage: "Planning",
+            command: "/research-plan",
+            expectedOutputs: ["plan_res.md"],
+            reason: "The project still needs a concrete Dataset / Model / Training / Testing plan before implementation.",
+        };
+    }
+    if (!snapshot.hasDataValidation) {
+        return {
+            stage: "Dataset validation",
+            command: "/dataset-validate",
+            expectedOutputs: ["data_validation.md"],
+            reason: "Data reality, splits, labels, and leakage risk should be reviewed separately before judging model quality.",
+        };
+    }
+    if (!snapshot.hasBaseline) {
+        return {
+            stage: "Baseline setup",
+            command: "/baseline-runner",
+            expectedOutputs: ["baseline_res.md", "experiments/baselines/"],
+            reason: "The project still lacks baseline results under a matched protocol, so headline comparisons would be too early.",
+        };
+    }
+    if (!snapshot.hasImplementationReport) {
+        return {
+            stage: "Implementation",
+            command: "/research-implement",
+            expectedOutputs: ["project/", "ml_res.md"],
+            reason: "The route, plan, data check, and baseline contract are already in place, so the next step is implementation plus 2-epoch validation.",
+        };
+    }
+    if (snapshot.latestReviewVerdict !== "PASS") {
+        return {
+            stage: "Review",
+            command: "/research-review",
+            expectedOutputs: ["iterations/judge_v{N}.md"],
+            reason: "Implementation exists, but review has not yet reached PASS, so model quality still needs a dedicated review pass.",
+        };
+    }
+    if (!snapshot.hasExperiment) {
+        return {
+            stage: "Full experiment",
+            command: "/research-experiment",
+            expectedOutputs: ["experiment_res.md", "experiment_analysis/"],
+            reason: "Implementation and review are ready, so the next step is full training, ablations, and supplementary experiments.",
+        };
+    }
+    return {
+        stage: "Experiment complete",
+        command: "/write-review-paper",
+        expectedOutputs: ["review/"],
+        reason: "The core ML execution chain is complete, so the project can move into synthesis, survey writing, or outward-facing summaries.",
+    };
+}
+function formatArtifactPresence(snapshot) {
+    const items = [
+        ["survey", snapshot.hasSurvey],
+        ["selection", snapshot.hasSelection],
+        ["plan", snapshot.hasPlan],
+        ["data_validation", snapshot.hasDataValidation],
+        ["baseline", snapshot.hasBaseline],
+        ["implement", snapshot.hasImplementationReport],
+        ["review", snapshot.latestReviewVerdict === "PASS"],
+        ["experiment", snapshot.hasExperiment],
+    ];
+    return items.map(([label, ok]) => `${ok ? "yes" : "no"} ${label}`).join(" | ");
+}
 /**
  * /research-status - Show workspace status for all research agents
  */
@@ -46,6 +185,8 @@ export function handleResearchStatus(_ctx) {
         const ideasCount = countFiles(path.join(w, "ideas"), (f) => f.endsWith(".md"));
         const topicCount = countFiles(path.join(w, "knowledge"), (f) => f.startsWith("topic-"));
         const hypothesisCount = countFiles(path.join(w, "ideas"), (f) => f.startsWith("hyp-"));
+        const snapshot = buildProjectSnapshot(w);
+        const next = inferNextAction(snapshot);
         let currentDay = 0;
         try {
             const config = JSON.parse(fs.readFileSync(path.join(w, "config.json"), "utf-8"));
@@ -54,7 +195,24 @@ export function handleResearchStatus(_ctx) {
         catch { /* not yet bootstrapped */ }
         output += `**${projectId}** (Day ${currentDay})\n`;
         output += `  Workspace: \`${w}\`\n`;
-        output += `  Topics: ${topicCount} | Hypotheses: ${hypothesisCount} | Papers: ${papersCount} | Ideas: ${ideasCount}\n\n`;
+        output += `  Topics: ${topicCount} | Hypotheses: ${hypothesisCount} | Papers: ${papersCount} | Ideas: ${ideasCount}\n`;
+        output += `  Stage: ${next.stage}\n`;
+        output += `  Artifacts: ${formatArtifactPresence(snapshot)}\n`;
+        output += `  Next: \`${next.command}\`\n`;
+        output += `  Why: ${next.reason}\n`;
+        output += `  Expected: ${next.expectedOutputs.map((p) => `\`${p}\``).join(", ")}\n`;
+        const gateStatus = readReleaseGateStatus(w);
+        if (hasReleaseFacingArtifacts(w) || gateStatus.state !== "missing") {
+            output += `  Release Gate: ${formatReleaseGateStatus(gateStatus)}\n`;
+            if (gateStatus.state === "stale" && gateStatus.staleReasons.length > 0) {
+                output += `  Gate Detail: ${gateStatus.staleReasons[0]}\n`;
+            }
+            const nextStep = getReleaseGateNextStep(w, gateStatus);
+            if (nextStep) {
+                output += `  Release Next: ${nextStep}\n`;
+            }
+        }
+        output += `\n`;
     }
     return { text: output };
 }

package/dist/src/commands.js.map

@@ -1 +1 @@
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package/dist/src/release-gate.d.ts

@@ -0,0 +1,14 @@
+export type ReleaseVerdict = "HOLD" | "CONDITIONAL_GO" | "GO";
+export interface ReleaseGateStatus {
+    state: "missing" | "invalid" | "fresh" | "stale";
+    verdict?: ReleaseVerdict;
+    gatePath: string;
+    checkedFiles: string[];
+    staleReasons: string[];
+    generatedAt?: string;
+}
+export declare function hasReleaseFacingArtifacts(workspace: string): boolean;
+export declare function readReleaseGateStatus(workspace: string): ReleaseGateStatus;
+export declare function formatReleaseGateStatus(status: ReleaseGateStatus): string;
+export declare function getReleaseGateNextStep(workspace: string, status: ReleaseGateStatus): string | null;
+//# sourceMappingURL=release-gate.d.ts.map

package/dist/src/release-gate.d.ts.map

@@ -0,0 +1 @@
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