psyclaw 0.28.3 → 0.29.2

package/dist/src/verify/checklist.js

@@ -0,0 +1,71 @@
+import { readFile } from "node:fs/promises";
+import { atomicWriteFile } from "../project/jsonl.js";
+import { assertSafeProjectPath } from "../project/paths.js";
+export const VERIFY_CHECKLIST_SCHEMA = "psyclaw/verify-checklist/v1";
+export const VERIFY_CHECKLIST_PATH = ".psyclaw/verify-checklist.json";
+const DEFAULT_ITEMS = [
+    { id: "n", label: "样本量 / N" },
+    { id: "primary-effect", label: "主效应 / 主要结果" },
+    { id: "table-text", label: "表与正文一致" },
+    { id: "method-match", label: "方法与实际分析一致" },
+    { id: "key-claim", label: "关键主张有结果支撑" },
+];
+export function defaultVerifyChecklist(now = new Date().toISOString()) {
+    return {
+        schemaVersion: VERIFY_CHECKLIST_SCHEMA,
+        updatedAt: now,
+        items: DEFAULT_ITEMS.map((item) => ({ ...item, status: "unverified" })),
+    };
+}
+export async function loadVerifyChecklist(root) {
+    const path = await assertSafeProjectPath(root, VERIFY_CHECKLIST_PATH);
+    try {
+        const parsed = JSON.parse(await readFile(path, "utf8"));
+        if (parsed.schemaVersion !== VERIFY_CHECKLIST_SCHEMA || !Array.isArray(parsed.items)) {
+            return defaultVerifyChecklist();
+        }
+        return {
+            schemaVersion: VERIFY_CHECKLIST_SCHEMA,
+            updatedAt: typeof parsed.updatedAt === "string" ? parsed.updatedAt : new Date().toISOString(),
+            items: parsed.items.filter((item) => Boolean(item && typeof item.id === "string" && typeof item.label === "string" &&
+                (item.status === "unverified" || item.status === "verified" || item.status === "flagged"))),
+        };
+    }
+    catch {
+        return defaultVerifyChecklist();
+    }
+}
+export async function saveVerifyChecklist(root, checklist) {
+    const path = await assertSafeProjectPath(root, VERIFY_CHECKLIST_PATH);
+    await atomicWriteFile(path, `${JSON.stringify(checklist, null, 2)}\n`);
+}
+export async function markVerifyItem(root, id, status, notes) {
+    const checklist = await loadVerifyChecklist(root);
+    const now = new Date().toISOString();
+    const existing = checklist.items.find((item) => item.id === id);
+    if (existing) {
+        existing.status = status;
+        existing.updatedAt = now;
+        if (notes !== undefined)
+            existing.notes = notes;
+    }
+    else {
+        const item = { id, label: id, status, updatedAt: now };
+        if (notes !== undefined)
+            item.notes = notes;
+        checklist.items.push(item);
+    }
+    checklist.updatedAt = now;
+    await saveVerifyChecklist(root, checklist);
+    return checklist;
+}
+export function formatVerifyChecklist(checklist) {
+    const lines = ["核查清单（AI 语义核查 + 人确认；非 SHA 学术过关）", `更新：${checklist.updatedAt}`];
+    for (const item of checklist.items) {
+        const mark = item.status === "verified" ? "[x]" : item.status === "flagged" ? "[!]" : "[ ]";
+        lines.push(`${mark} ${item.id}: ${item.label}${item.notes ? ` — ${item.notes}` : ""}`);
+    }
+    lines.push("用法：/verify list | /verify <id> verified|unverified|flagged [备注]");
+    return lines.join("\n");
+}
+//# sourceMappingURL=checklist.js.map

package/dist/src/verify/checklist.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "psyclaw",
-  "version": "0.28.3",
+  "version": "0.29.2",
   "description": "A standalone, evidence-grounded social-science research agent with research contracts, evidence gates, and recoverable workflows",
   "type": "module",
   "license": "MIT",
@@ -73,6 +73,7 @@
     "test:watch": "vitest",
     "eval": "tsx evals/harness.ts",
     "eval:modules": "tsx evals/modules.ts",
+    "eval:academic-route": "tsx evals/academic-soft-route/harness.ts",
     "rebrand": "node scripts/rebrand-pi.mjs",
     "check:branding": "node scripts/check-branding.mjs",
     "release:push": "node scripts/release-push.mjs",

package/scripts/rebrand-pi.mjs

@@ -165,7 +165,7 @@ const logo = [
   "",
 ].join("\\n");`;
 
-const GRAD_CORE_SKILLS = "\\x1b[1m\\x1b[38;2;56;189;248m✦ 核心证据链:\\x1b[0m \\x1b[1m\\x1b[38;2;56;189;248mresearch-intake\\x1b[0m \\x1b[38;2;99;102;241m➔\\x1b[0m \\x1b[1m\\x1b[38;2;129;140;248mevidence-capture\\x1b[0m \\x1b[38;2;168;85;247m➔\\x1b[0m \\x1b[1m\\x1b[38;2;168;85;247mcitation-audit\\x1b[0m \\x1b[38;2;236;72;153m➔\\x1b[0m \\x1b[1m\\x1b[38;2;45;212;191mresearch-brief\\x1b[0m";
+const GRAD_CORE_SKILLS = "\\x1b[1m\\x1b[38;2;56;189;248m✦ 核心证据链:\\x1b[0m \\x1b[1m\\x1b[38;2;56;189;248mresearch-intake\\x1b[0m \\x1b[38;2;99;102;241m➔\\x1b[0m \\x1b[1m\\x1b[38;2;129;140;248mevidence-capture\\x1b[0m \\x1b[38;2;168;85;247m➔\\x1b[0m \\x1b[1m\\x1b[38;2;168;85;247mcitation-audit\\x1b[0m";
 
 const PSYCLAW_SKILLS_FORMATTER = `const skills = skillsResult.skills;
             if (skills.length > 0) {
@@ -174,7 +174,7 @@ const PSYCLAW_SKILLS_FORMATTER = `const skills = skillsResult.skills;
                     formatPath: (item) => this.formatDisplayPath(item.path),
                     formatPackagePath: (item) => this.getShortPath(item.path, item.sourceInfo),
                 });
-                const CORE_PIPELINE = ["research-intake", "evidence-capture", "citation-audit", "research-brief"];
+                const CORE_PIPELINE = ["research-intake", "evidence-capture", "citation-audit"];
                 const availableCore = CORE_PIPELINE.filter((name) => skills.some((s) => s.name === name));
                 const otherSkills = skills.filter((s) => !CORE_PIPELINE.includes(s.name)).map((s) => s.name);
                 const skillCompactList = \`  ${GRAD_CORE_SKILLS}\\n\${theme.fg("dim", \`  ⟡ 生态扩展 (\${otherSkills.length}): \${otherSkills.slice(0, 10).join(", ")}\${otherSkills.length > 10 ? " ... (按 Ctrl+O 展开全部)" : ""}\`)}\`;

package/skills/core/academic-grill/SKILL.md

@@ -17,7 +17,7 @@ When the user provides a dataset or topic without a mature research question, be
 - Resolve upstream decisions before downstream ones. Do not ask about an analysis technique while the construct, estimand, comparison, or data-generating process is still unclear.
 - If the answer can be established from files, project state, registered evidence, code, or prior conversation, inspect those sources instead of asking the user.
 - Enter a researcher decision only when at least two substantively defensible options remain after checking the available evidence and established methods, and the choice would change the research question, sample treatment, operationalization, estimand, analysis method, or interpretation. Record what evidence and methods were checked, explain why they cannot resolve the disagreement, and state the options, evidence, consequences, and your recommendation.
-- Do not ask the researcher to decide software installation, dependency repair, file formatting, script debugging, reproducibility metadata, citation formatting, or a reporting omission that the agent can repair. Repair these directly inside an active `/run`, or report a concrete technical limitation without treating it as a research decision.
+- Do not ask the researcher to decide software installation, dependency repair, file formatting, script debugging, reproducibility metadata, citation formatting, or a reporting omission that the agent can repair. Repair these directly after `/init`, or report a concrete technical limitation without treating it as a research decision.
 - A dataset supplied for analysis is exploratory by default unless the user says that hypotheses and analyses were fixed before seeing it. Do not lead with a preregistration question, do not ask for a preregistration URL, and do not imply that exploratory work is methodologically inferior. For explicitly confirmatory work, ask what was specified in advance only when that distinction affects analysis or interpretation.
 - Use researcher-facing language. Keep internal terms such as Claim, Evidence, ledger, gate, audit, blocked, receipt, and dependency out of ordinary questions and proposed prose.
 - Use the user's latest answer to choose the next unresolved branch. Do not dump a static questionnaire.

package/skills/core/analysis-plan/SKILL.md

@@ -0,0 +1,29 @@
+---
+name: analysis-plan
+description: Soft-takeover stats planning in analysis mode — light EDA, clarifying questions, structured proposal, soft confirm, review, then run now or later via local scripts (MCP only when needed).
+license: MIT
+---
+
+# Analysis Plan
+
+Use this skill only in **analysis** mode. Do not start academic/ARS writing from here.
+
+## Stages
+
+1. **Clarify + light EDA** — Inspect available data under `data/clean` (or documented paths). Write a short profile (shape, dtypes, missingness, key ranges) once; do not spam ad-hoc probes. Ask only high-value clarifying questions that change the estimand, sample treatment, or method family.
+2. **Propose** — Produce a structured plan: goal, confirmatory vs exploratory, primary outcome, primary analysis, alternatives considered, missing-data / multiplicity / exclusion notes, and proposed script layout under `analysis/scripts/`.
+3. **Soft confirm** — Present the proposal clearly and ask the researcher to confirm with `/plan confirm <method>` (or reject). Soft confirm is not an ARS checkpoint and not a hard `awaiting-human` safety gate.
+4. **Review** — Run `/plan review` (or ask the user to). Fix warn/block findings before execution.
+5. **Execute** — `/plan run` (now) or `/plan defer` (later). Default backend: **local reproducible scripts** using mature libraries (pandas / pingouin / statsmodels / scipy, or R equivalents). Use MCP only for special backends (SPSS / Mplus / MNE / Stata) or when the user explicitly asks.
+6. **Handoff** — After results exist, update `analysis/HANDOFF.md` (`/plan handoff`) before the user switches to academic mode. Academic mode must consume the handoff and must not re-choose primary tests.
+
+## Persistence
+
+Keep durable state in `analysis/plans/` via `/plan` commands (`new`, `status`, `confirm`, `review`, `run`, `defer`, `handoff`). Prefer thin entrypoints (`run_all.py`) and reviewable modules; never invent numerical results.
+
+## Boundaries
+
+- Never overwrite `data/raw`.
+- Never implement novel statistical algorithms inside PsyClaw core; call libraries or trusted MCP.
+- Do not merge this plan with ARS stage planning.
+- Label unverified claims; use `/verify` for human marks on critical fields.

package/skills/core/manifest.json

@@ -1,15 +1,15 @@
 {
   "schemaVersion": "psyclaw/skill-pack/v1",
   "id": "psyclaw-core",
-  "version": "0.2.0",
+  "version": "0.3.0",
   "skills": [
     "academic-grill",
     "research-intake",
     "evidence-capture",
     "citation-audit",
-    "research-brief"
+    "analysis-plan"
   ],
-  "enabledByDefault": ["academic-grill", "research-intake", "evidence-capture", "citation-audit", "research-brief"],
+  "enabledByDefault": ["academic-grill", "research-intake", "evidence-capture", "citation-audit", "analysis-plan"],
   "source": {"kind": "workspace", "ref": "initial-mvp"},
   "license": {"spdx": "MIT", "evidenceRef": "../../LICENSE"},
   "dependencyStatus": "ready"

package/vendor/ars/pi/wrapper.js

@@ -173,29 +173,38 @@ export default function (pi) {
       const python = await probe(pi, "python3", ["--version"]);
       const pyyaml = await probe(pi, "python3", ["-c", "import yaml; print(f'PyYAML {yaml.__version__}')"]);
       const pandoc = await probe(pi, "pandoc", ["--version"]);
-      const tectonic = await probe(pi, "tectonic", ["--version"]);
       const sandbox = pi.getCommands().some((command) => command.name === "sandbox")
         ? `detected; allow read access to ${repoRoot} when running outside the checkout`
         : "not detected";
       const format = (matches) => matches.length > 0 ? matches.join(", ") : "none; sequential/degraded mode";
+      const psyclawOrch = [
+        ...uniqueMatches(candidates, /psyclaw_ars_multi_agent|ars multi-agent|parallel-agent/i),
+        ...commands.filter((item) => /agents|create-subagent/i.test(item.search)).map((item) => item.label),
+      ];
+      const orchestrationLine = psyclawOrch.length > 0
+        ? psyclawOrch.join(", ")
+        : format(orchestration);
       const report = [
         "ARS Pi doctor",
         `Repository: ${repoRoot}`,
-        `Orchestration: ${format(orchestration)}`,
+        `Orchestration: ${orchestrationLine}`,
         `Web retrieval: ${format(web)}`,
         `Python: ${python}`,
         `PyYAML: ${pyyaml}`,
         `Pandoc: ${pandoc}`,
-        `Tectonic: ${tectonic}`,
+        "PDF engine: not preflighted; install on demand when the user asks to export PDF (psyclaw_ensure_pdf_engine)",
         `Sandbox: ${sandbox}`,
-        "Claude hooks: unavailable in Pi; write-scope enforcement remains prompt-level",
+        "Hooks: PsyClaw analysis hooks + tool_call gates after /init; Claude Code PreToolUse hooks.json is not loaded by Pi",
       ].join("\n");
 
       pi.sendMessage({ customType: "ars-pi-doctor", content: report, display: true });
     },
   });
 
-  pi.on("before_agent_start", (event) => {
+  pi.on("before_agent_start", (event, ctx) => {
+    // Keep in-memory flag aligned with session entries written by PsyClaw Shift+Tab
+    // (silent appendEntry) or prior /ars-pi-start|/ars-pi-stop handlers.
+    if (ctx?.sessionManager) restoreArsState(ctx);
     if (!arsActive) return { systemPrompt: hideArsSkills(event.systemPrompt) };
     return { systemPrompt: `${event.systemPrompt}\n${compatibility}` };
   });

package/vendor/ars/pi/wrapper.test.mjs

@@ -199,3 +199,13 @@ test("/ars-pi-start and /ars-pi-stop toggle automatic invocation", async () => {
     assert.equal(runBeforeAgentStart(harness).includes(location), false);
   }
 });
+
+test("before_agent_start restores ARS state from session entries (silent Shift+Tab path)", () => {
+  const harness = createHarness();
+  harness.setBranch([{ type: "custom", customType: "ars-pi-state", data: { active: true } }]);
+  const systemPrompt = harness.handlers.get("before_agent_start")(
+    { systemPrompt: baseSystemPrompt },
+    harness.sessionContext,
+  )?.systemPrompt ?? baseSystemPrompt;
+  assert.equal(systemPrompt.includes(compatibilityMarker), true);
+});

package/dist/src/research/brief.d.ts

@@ -1,11 +0,0 @@
-import type { GateResult, Handoff } from "../core/contracts.js";
-export interface BriefResult {
-    runId: string;
-    verdict: "pass" | "blocked";
-    gates: GateResult[];
-    briefPath?: string;
-    manifestPath: string;
-    verdictPath: string;
-    handoff: Handoff;
-}
-export declare function runOfflineBrief(root: string): Promise<BriefResult>;

package/dist/src/research/brief.js

@@ -1,81 +0,0 @@
-import { mkdir } from "node:fs/promises";
-import { join } from "node:path";
-import { randomUUID } from "node:crypto";
-import { checkEvidenceSufficiency } from "../core/evidence-policy.js";
-import { projectPaths } from "../project/paths.js";
-import { loadLedger, readProject } from "./ledger.js";
-import { writeHandoff } from "../project/bootstrap.js";
-import { atomicWriteFile } from "../project/jsonl.js";
-import { RunEventLog } from "../panel/events.js";
-export async function runOfflineBrief(root) {
-    const paths = projectPaths(root);
-    const runId = `run_${randomUUID().replaceAll("-", "")}`;
-    const project = await readProject(root);
-    const ledger = await loadLedger(root);
-    const gates = checkEvidenceSufficiency({ ...ledger, paradigm: project.paradigm });
-    const blocked = gates.filter((gate) => !gate.ok);
-    const eventLog = new RunEventLog(root, runId);
-    const eventAt = new Date().toISOString();
-    await eventLog.append({ type: "planned", at: eventAt });
-    for (const gate of gates)
-        await eventLog.append({ type: "gate", at: eventAt, message: gate.reason });
-    await eventLog.append({
-        type: blocked.length === 0 ? "completed" : "blocked",
-        at: eventAt,
-        message: blocked.length === 0 ? "all evidence gates passed" : "evidence gates blocked",
-    });
-    const manifest = {
-        schemaVersion: "psyclaw/brief-manifest/v1",
-        runId,
-        inputs: ledger.evidence.map((item) => ({ id: item.id, sha256: item.sha256, locator: item.source.locator })),
-        claims: ledger.claims.map((claim) => ({ id: claim.id, status: claim.status, evidenceIds: claim.evidenceIds })),
-        gates,
-        generatedAt: new Date().toISOString(),
-    };
-    await mkdir(paths.manifests, { recursive: true });
-    const manifestPath = join(paths.manifests, `${runId}.json`);
-    await atomicWriteFile(manifestPath, `${JSON.stringify(manifest, null, 2)}\n`);
-    let briefPath;
-    if (blocked.length === 0) {
-        const goal = project.goal;
-        const lines = [
-            "# Research Brief",
-            "",
-            `Research goal: ${goal}`,
-            "",
-            "## Audited Claims",
-            "",
-            ...ledger.claims.map((claim) => `- ${claim.text} [${claim.status}]`),
-            "",
-            "Evidence and limitations are recorded in the manifest and ledger.",
-            "",
-        ];
-        briefPath = join(paths.outputs, "brief.md");
-        await atomicWriteFile(briefPath, lines.join("\n"));
-    }
-    const verdictPath = join(paths.manifests, `${runId}.verdict.json`);
-    const verdict = {
-        schemaVersion: "psyclaw/verdict/v1",
-        runId,
-        verdict: blocked.length === 0 ? "pass" : "blocked",
-        manifestPath,
-        ...(briefPath ? { briefPath } : {}),
-        gateCount: gates.length,
-        blockedGateCount: blocked.length,
-        generatedAt: new Date().toISOString(),
-    };
-    await atomicWriteFile(verdictPath, `${JSON.stringify(verdict, null, 2)}\n`);
-    const handoff = await writeHandoff(root, {
-        projectId: project.id,
-        runId,
-        goal: project.goal,
-        completed: ["evidence ledger loaded", "evidence sufficiency gates evaluated"],
-        verified: blocked.length === 0 ? ["brief.md", "manifest", "verdict"] : ["manifest", "verdict"],
-        blocked: blocked.map((gate) => gate.reason),
-        nextSteps: blocked.length === 0 ? ["review before external use"] : ["retrieve missing evidence, narrow unsupported statements, and rerun the checks"],
-        verificationCommands: ["pnpm typecheck", "pnpm test"],
-        generatedAt: new Date().toISOString(),
-    });
-    return { runId, verdict: blocked.length === 0 ? "pass" : "blocked", gates, ...(briefPath ? { briefPath } : {}), manifestPath, verdictPath, handoff };
-}
-//# sourceMappingURL=brief.js.map

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

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package/skills/core/research-brief/SKILL.md

@@ -1,17 +0,0 @@
----
-name: research-brief
-description: Produce a concise, evidence-grounded research brief from an approved intake card and audited local evidence ledger.
-license: MIT
----
-
-# Research Brief
-
-Follow intake -> capture -> ledger -> audit -> write -> handoff. Write only from accepted evidence and label gaps, contradictions, exploratory claims, and human decisions. Include a provenance manifest, verification verdict, and executable handoff; do not invent citations, data, methods, or numerical results.
-
-For manuscript outputs, use continuous academic paragraphs rather than bullet-heavy notes. Apply a neutral submission format: Times New Roman for Latin text, SimSun/宋体 fallback for Chinese, black headings and body text, and no decorative color. Before finalization, ensure each factual or literature-dependent paragraph has a verified citation; if sources are insufficient, retrieve more or mark the section uncertain instead of fabricating references.
-
-Keep internal workflow language out of reader-facing prose. Translate Claim/Evidence checks into ordinary scholarly reasoning and avoid bureaucratic terms such as audit, blocked outcome, dependency, receipt, or gate. In Chinese psychology writing, prefer context-specific terms such as research statement, supporting literature, quality check, outcome variable or indicator, required software, and unavailable analysis. Remove stacked modifiers and repeated methodological disclaimers; state each necessary limitation once in the most relevant section.
-
-Follow the target venue's abstract instructions exactly. Without a supplied venue format, write one concise paragraph covering purpose, method, principal results, and conclusion; do not add explicit four-part labels by default. Keep column-level data diagnostics, hashes, implementation details, and exhaustive secondary results out of the abstract. Report data quality in aggregate in the manuscript and put complete variable-level diagnostics in supplementary material.
-
-Reference use is part of the manuscript, not a separate inventory. Apply one citation style consistently, make every in-text citation match exactly one reference entry and vice versa, preserve the publication type, and verify author order, year, title, journal or proceedings, volume, issue, pages or article number, DOI, punctuation, ordering, and hanging indent from source metadata. Never fill missing fields from memory.