research-copilot 0.2.17 → 0.2.21

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "research-copilot",
-  "version": "0.2.17",
+  "version": "0.2.21",
   "description": "AI-powered research assistant for scientists — literature search, data analysis, academic writing, and project management",
   "type": "module",
   "bin": {

package/scripts/audit-diagram-prompts.mjs

@@ -0,0 +1,67 @@
+#!/usr/bin/env node
+import { readdirSync, readFileSync, statSync } from 'node:fs'
+import { join, resolve } from 'node:path'
+
+const SUSPECT_TERMS = [
+  'dataset', 'datasets', 'training data', 'test set', 'validation set',
+  'experiment', 'experiments', 'experimental setup', 'hyperparameter', 'hyperparameters',
+  'accuracy', 'precision', 'recall', 'F1', 'AUC', 'PSNR', 'BLEU', 'ROUGE',
+  'ablation', 'ablations',
+  'baseline', 'baselines', 'SOTA', 'state-of-the-art', 'benchmark',
+  'GPU', 'A100', 'V100', 'epochs', 'batch size', 'learning rate',
+  'Table 1', 'Table 2', 'Figure 1', 'Figure 2',
+  'outperforms', 'achieves', '%',
+]
+
+function findLogs(root) {
+  const out = []
+  const walk = (dir) => {
+    let entries
+    try { entries = readdirSync(dir, { withFileTypes: true }) } catch { return }
+    for (const e of entries) {
+      const p = join(dir, e.name)
+      if (e.isDirectory()) {
+        if (e.name === 'node_modules' || e.name.startsWith('.')) continue
+        walk(p)
+      } else if (e.isFile() && e.name.endsWith('_review_log.json')) {
+        out.push(p)
+      }
+    }
+  }
+  walk(root)
+  return out
+}
+
+const root = resolve(process.argv[2] || process.cwd())
+const logs = findLogs(root).sort((a, b) => statSync(b).mtimeMs - statSync(a).mtimeMs)
+
+if (logs.length === 0) {
+  console.error(`No *_review_log.json under ${root}`)
+  process.exit(1)
+}
+
+console.log(`# Prompt audit — ${logs.length} log file(s) under ${root}\n`)
+
+for (const file of logs) {
+  let data
+  try { data = JSON.parse(readFileSync(file, 'utf-8')) } catch (e) {
+    console.log(`## ${file}\nPARSE ERROR: ${e.message}\n`); continue
+  }
+  const prompt = String(data.prompt ?? '')
+  const len = prompt.length
+  const wordCount = prompt.split(/\s+/).filter(Boolean).length
+  const lower = prompt.toLowerCase()
+  const hits = SUSPECT_TERMS.filter(t => {
+    const re = new RegExp(`\\b${t.toLowerCase().replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\$&')}\\b`)
+    return re.test(lower)
+  })
+  const finalScore = data.iterations?.at(-1)?.review?.score ?? '—'
+  const verdict = data.iterations?.at(-1)?.review?.verdict ?? '—'
+
+  console.log(`## ${file.replace(root + '/', '')}`)
+  console.log(`- length: ${len} chars / ${wordCount} words`)
+  console.log(`- docType: ${data.docType} | diagramType: ${data.diagramType} | aspect: ${data.aspect}`)
+  console.log(`- final: score=${finalScore} verdict=${verdict} stoppedReason=${data.stoppedReason ?? '—'}`)
+  console.log(`- suspect terms (${hits.length}): ${hits.length ? hits.join(', ') : '—'}`)
+  console.log(`\n### prompt verbatim\n\n\`\`\`\n${prompt}\n\`\`\`\n`)
+}

package/scripts/test-skill-routing.mjs

@@ -0,0 +1,238 @@
+#!/usr/bin/env node
+// Smoke test for the coordinator's LLM-based skill router.
+//
+// Reproduces `matchSkillsWithLLM` in lib/agents/coordinator.ts verbatim:
+//   - Same system prompt
+//   - Same `- <name>: <description>` skill list
+//   - Same router-model class (Haiku / GPT-5-nano / Gemini-2.0-flash-lite)
+//   - Same JSON-array parse
+//
+// Usage:
+//   node scripts/test-skill-routing.mjs            # anthropic (default), needs ANTHROPIC_API_KEY
+//   node scripts/test-skill-routing.mjs --provider=openai    # needs OPENAI_API_KEY
+//   node scripts/test-skill-routing.mjs --provider=google    # needs GEMINI_API_KEY
+//   node scripts/test-skill-routing.mjs --cases=path/to/cases.json
+//
+// Exits non-zero if any case fails (expected skill missing, or forbidden skill present).
+
+import { readdirSync, readFileSync, existsSync } from 'fs'
+import { join, dirname } from 'path'
+import { fileURLToPath } from 'url'
+import { getModel, getEnvApiKey, completeSimple } from '@mariozechner/pi-ai'
+
+const __dirname = dirname(fileURLToPath(import.meta.url))
+const REPO_ROOT = join(__dirname, '..')
+const BUILTIN_SKILLS_DIR = join(REPO_ROOT, 'lib', 'skills', 'builtin')
+
+// ---------------------------------------------------------------------------
+// CLI args
+// ---------------------------------------------------------------------------
+
+const args = Object.fromEntries(
+  process.argv.slice(2).map(a => {
+    const [k, v = 'true'] = a.replace(/^--/, '').split('=')
+    return [k, v]
+  })
+)
+
+const PROVIDER = args.provider ?? 'anthropic'
+const CASES_PATH = args.cases
+
+const ROUTER_BY_PROVIDER = {
+  anthropic: 'claude-haiku-4-5-20251001',
+  openai: 'gpt-5.4-nano',
+  google: 'gemini-2.0-flash-lite'
+}
+
+// ---------------------------------------------------------------------------
+// Skill discovery — mirrors lib/skills/loader.ts frontmatter parse
+// ---------------------------------------------------------------------------
+
+function parseFrontmatter(md) {
+  if (!md.startsWith('---')) return null
+  const end = md.indexOf('\n---', 3)
+  if (end < 0) return null
+  const fm = md.slice(3, end).trim()
+  const out = {}
+  for (const line of fm.split('\n')) {
+    const m = line.match(/^(\w[\w-]*):\s*(.*)$/)
+    if (!m) continue
+    let v = m[2].trim()
+    if (v.startsWith('"') && v.endsWith('"')) v = v.slice(1, -1)
+    out[m[1]] = v
+  }
+  return out
+}
+
+function loadBuiltinSkills() {
+  const skills = []
+  for (const name of readdirSync(BUILTIN_SKILLS_DIR)) {
+    const skillFile = join(BUILTIN_SKILLS_DIR, name, 'SKILL.md')
+    if (!existsSync(skillFile)) continue
+    const md = readFileSync(skillFile, 'utf-8')
+    const fm = parseFrontmatter(md)
+    if (!fm?.name || !fm?.description) continue
+    skills.push({ name: fm.name, description: fm.description })
+  }
+  return skills.sort((a, b) => a.name.localeCompare(b.name))
+}
+
+// ---------------------------------------------------------------------------
+// Exact copy of matchSkillsWithLLM prompt (coordinator.ts:99-148)
+// ---------------------------------------------------------------------------
+
+const MAX_SKILL_PRELOAD = 5
+
+function buildSystemPrompt(skills) {
+  const skillList = skills.map(s => `- ${s.name}: ${s.description}`).join('\n')
+  return [
+    'You are a skill router for a research assistant. Given a user message, select which skills should be activated.',
+    'Return ONLY a JSON array of skill names. Return [] if none are relevant.',
+    '',
+    'Rules:',
+    '- Only select skills directly relevant to the user\'s request',
+    '- Do not select skills speculatively',
+    `- Maximum ${MAX_SKILL_PRELOAD} skills`,
+    '- Consider both English and Chinese messages',
+    '',
+    'Available skills:',
+    skillList
+  ].join('\n')
+}
+
+async function routeOnce(model, apiKey, systemPrompt, message) {
+  const result = await completeSimple(model, {
+    systemPrompt,
+    messages: [{ role: 'user', content: message, timestamp: Date.now() }]
+  }, { maxTokens: 100, apiKey })
+
+  const textContent = result.content.find(c => c.type === 'text')
+  const text = textContent?.text?.trim() ?? ''
+  if (!text) return { raw: '', picked: [] }
+
+  const jsonMatch = text.match(/```(?:json)?\s*([\s\S]*?)```/) ?? text.match(/(\[[\s\S]*?\])/)
+  const jsonStr = jsonMatch?.[1]?.trim() ?? text
+  try {
+    const parsed = JSON.parse(jsonStr)
+    if (!Array.isArray(parsed)) return { raw: text, picked: [] }
+    return {
+      raw: text,
+      picked: parsed.filter(n => typeof n === 'string').slice(0, MAX_SKILL_PRELOAD)
+    }
+  } catch {
+    return { raw: text, picked: [] }
+  }
+}
+
+// ---------------------------------------------------------------------------
+// Test cases — focused on the two new marp skills
+// ---------------------------------------------------------------------------
+
+const DEFAULT_CASES = [
+  {
+    msg: "let's work in week10_dist folder, create a new week10B_storage_design_slides_v2.md for teaching next week. You can check other docs in the week10_dist folder as your references and write high quality teaching slides.",
+    expect: ['teaching-marp-slides'],
+    forbid: ['academic-marp-slides']
+  },
+  {
+    msg: 'Make lecture slides for CS101 on backpropagation',
+    expect: ['teaching-marp-slides'],
+    forbid: ['academic-marp-slides']
+  },
+  {
+    msg: '我要做个论文答辩 PPT',
+    expect: ['academic-marp-slides'],
+    forbid: ['teaching-marp-slides']
+  },
+  {
+    msg: '下周课件，讲 LR 和 logistic regression',
+    expect: ['teaching-marp-slides'],
+    forbid: ['academic-marp-slides']
+  },
+  {
+    msg: 'slides for my group meeting',
+    expect: ['academic-marp-slides'],
+    forbid: ['teaching-marp-slides']
+  },
+  {
+    msg: 'revise slide 7 of my conference talk',
+    expect: ['academic-marp-slides'],
+    forbid: ['teaching-marp-slides']
+  },
+  {
+    msg: 'add a worked example to my lecture slides',
+    expect: ['teaching-marp-slides'],
+    forbid: ['academic-marp-slides']
+  },
+  {
+    msg: 'help me draft a NeurIPS paper intro',
+    expect: ['paper-writing'],
+    forbid: ['academic-marp-slides', 'teaching-marp-slides']
+  }
+]
+
+// ---------------------------------------------------------------------------
+// Main
+// ---------------------------------------------------------------------------
+
+async function main() {
+  const skills = loadBuiltinSkills()
+  console.log(`Loaded ${skills.length} builtin skills from ${BUILTIN_SKILLS_DIR}`)
+  const marpOnes = skills.filter(s => s.name.includes('marp'))
+  for (const s of marpOnes) console.log(`  • ${s.name}`)
+  console.log()
+
+  const routerModelId = ROUTER_BY_PROVIDER[PROVIDER]
+  if (!routerModelId) {
+    console.error(`Unknown provider "${PROVIDER}". Pick one of: ${Object.keys(ROUTER_BY_PROVIDER).join(', ')}`)
+    process.exit(2)
+  }
+  const apiKey = getEnvApiKey(PROVIDER)
+  if (!apiKey) {
+    console.error(`No API key for provider "${PROVIDER}" in env. Set the provider's standard env var (e.g., ANTHROPIC_API_KEY / OPENAI_API_KEY / GEMINI_API_KEY).`)
+    process.exit(2)
+  }
+  const model = getModel(PROVIDER, routerModelId)
+  console.log(`Using router: ${PROVIDER}/${routerModelId}\n`)
+
+  const cases = CASES_PATH
+    ? JSON.parse(readFileSync(CASES_PATH, 'utf-8'))
+    : DEFAULT_CASES
+
+  const systemPrompt = buildSystemPrompt(skills)
+
+  let failures = 0
+  for (const [i, c] of cases.entries()) {
+    process.stdout.write(`[${i + 1}/${cases.length}] "${c.msg}" ... `)
+    let result
+    try {
+      result = await routeOnce(model, apiKey, systemPrompt, c.msg)
+    } catch (err) {
+      console.log('ERROR')
+      console.log(`  ${err?.message ?? err}`)
+      failures++
+      continue
+    }
+
+    const picked = new Set(result.picked)
+    const missing = (c.expect ?? []).filter(name => !picked.has(name))
+    const forbidHits = (c.forbid ?? []).filter(name => picked.has(name))
+    const ok = missing.length === 0 && forbidHits.length === 0
+
+    console.log(ok ? 'PASS' : 'FAIL')
+    console.log(`  picked: [${result.picked.join(', ')}]`)
+    if (c.expect?.length) console.log(`  expect: [${c.expect.join(', ')}]`)
+    if (c.forbid?.length) console.log(`  forbid: [${c.forbid.join(', ')}]`)
+    if (missing.length) console.log(`  MISSING: [${missing.join(', ')}]`)
+    if (forbidHits.length) console.log(`  UNWANTED: [${forbidHits.join(', ')}]`)
+    if (!ok) failures++
+  }
+
+  console.log(`\n${cases.length - failures}/${cases.length} passed`)
+  process.exit(failures === 0 ? 0 : 1)
+}
+
+main().catch(err => {
+  console.error(err)
+  process.exit(1)
+})