@kernel.chat/kbot 3.51.0 → 3.54.0

package/dist/lab.js

@@ -0,0 +1,1020 @@
+// kbot Lab — Interactive Science REPL
+//
+// A specialized REPL mode for scientific research. Manages lab sessions
+// with domain-specific system prompts, automatic citation extraction,
+// variable tracking, and notebook export.
+//
+// Usage:
+//   $ kbot lab                    # Start a general science lab
+//   $ kbot lab --domain physics   # Start in physics domain
+//   $ kbot lab --resume <id>      # Resume a previous session
+//   $ kbot lab --name "QFT Notes" # Start a named session
+//
+// REPL commands:
+//   /domain <name>      — Switch scientific domain
+//   /notebook            — Show the current notebook
+//   /export [format]     — Export as markdown, latex, or json
+//   /cite <doi>          — Add a citation
+//   /hypothesis <text>   — Record a hypothesis
+//   /note <text>         — Add a research note
+//   /variables           — Show stored variables
+//   /set <name> <value>  — Store a variable
+//   /history             — List past lab sessions
+//   /resume <id>         — Resume a previous session
+//   /clear               — Clear current session
+//   /help                — Show lab commands
+//   /quit                — Exit the lab
+import { createInterface } from 'node:readline';
+import { homedir } from 'node:os';
+import { join } from 'node:path';
+import { existsSync, readFileSync, writeFileSync, mkdirSync, readdirSync, unlinkSync, } from 'node:fs';
+import chalk from 'chalk';
+import { runAgent } from './agent.js';
+import { gatherContext } from './context.js';
+import { printError, printInfo } from './ui.js';
+// ── Constants ──
+const LAB_DIR = join(homedir(), '.kbot', 'lab', 'sessions');
+const MAX_LAB_SESSIONS = 100;
+// ── Domain Configuration ──
+const DOMAIN_LABELS = {
+    physics: 'Physics',
+    chemistry: 'Chemistry',
+    biology: 'Biology',
+    math: 'Mathematics',
+    neuro: 'Neuroscience',
+    earth: 'Earth Science',
+    social: 'Social Science',
+    humanities: 'Humanities',
+    health: 'Health & Medicine',
+    general: 'General Science',
+};
+const DOMAIN_ICONS = {
+    physics: '\u269B\uFE0F', // atom
+    chemistry: '\u2697\uFE0F', // alembic
+    biology: '\uD83E\uDDEC', // dna
+    math: '\uD83D\uDCD0', // triangular ruler
+    neuro: '\uD83E\uDDE0', // brain
+    earth: '\uD83C\uDF0D', // globe
+    social: '\uD83D\uDC65', // people
+    humanities: '\uD83D\uDCDA', // books
+    health: '\u2695\uFE0F', // medical
+    general: '\uD83D\uDD2C', // microscope
+};
+const DOMAIN_COLORS = {
+    physics: '#60A5FA', // blue
+    chemistry: '#4ADE80', // green
+    biology: '#A78BFA', // violet
+    math: '#FBBF24', // amber
+    neuro: '#F472B6', // pink
+    earth: '#34D399', // emerald
+    social: '#FB923C', // orange
+    humanities: '#E879F9', // fuchsia
+    health: '#F87171', // red
+    general: '#67E8F9', // cyan
+};
+const DOMAIN_AGENTS = {
+    physics: 'researcher',
+    chemistry: 'researcher',
+    biology: 'researcher',
+    math: 'analyst',
+    neuro: 'researcher',
+    earth: 'researcher',
+    social: 'analyst',
+    humanities: 'writer',
+    health: 'researcher',
+    general: 'researcher',
+};
+/** Build a domain-specific system prompt that primes the agent for scientific work */
+function buildDomainPrompt(domain, session) {
+    const base = `You are a scientific research assistant operating in kbot lab mode.
+Domain: ${DOMAIN_LABELS[domain]}
+Session: "${session.name}" (started ${new Date(session.startedAt).toLocaleDateString()})
+
+IMPORTANT CONVENTIONS:
+- Always cite sources with DOIs or arXiv IDs when referencing specific findings
+- Use precise scientific terminology appropriate to ${DOMAIN_LABELS[domain]}
+- When presenting numeric results, include units and significant figures
+- Distinguish between established findings, recent results, and speculative claims
+- Format mathematical expressions using standard notation
+- When computations are performed, show the work step by step
+- If you reference a paper, include: authors, year, title, journal/source, and DOI if known`;
+    const domainSpecific = {
+        physics: `
+PHYSICS-SPECIFIC GUIDANCE:
+- Use SI units by default; convert to natural units when appropriate for HEP/QFT
+- For quantum mechanics: use Dirac notation where helpful
+- For classical mechanics: specify coordinate systems and reference frames
+- Dimensional analysis should accompany any derived formula
+- Preferred tools: symbolic computation, unit conversion, physics constants lookup
+- When discussing experiments, note the energy scale, detector type, and statistical significance`,
+        chemistry: `
+CHEMISTRY-SPECIFIC GUIDANCE:
+- Use IUPAC nomenclature for compounds
+- Include molecular formulas, structural info when relevant
+- For reactions: balance equations, specify conditions (temperature, pressure, catalyst)
+- Note safety considerations (GHS hazard codes) for hazardous substances
+- Preferred tools: compound search, reaction lookup, stoichiometry calc, spectroscopy data
+- For organic chemistry: specify stereochemistry where relevant`,
+        biology: `
+BIOLOGY-SPECIFIC GUIDANCE:
+- Use standard gene/protein nomenclature (HGNC for human genes, italic for genes)
+- For sequences: specify organism, accession numbers
+- For ecology: note sample sizes, confidence intervals, effect sizes
+- For cell biology: specify cell type, organism, culture conditions
+- Preferred tools: gene lookup, BLAST search, pathway search, taxonomy lookup
+- Always distinguish in vitro, in vivo, and in silico results`,
+        math: `
+MATHEMATICS-SPECIFIC GUIDANCE:
+- State theorems precisely with all hypotheses
+- Distinguish between definitions, lemmas, theorems, corollaries, and conjectures
+- Provide proofs or proof sketches when asked
+- Use standard notation (LaTeX-compatible) for expressions
+- Preferred tools: symbolic computation, OEIS lookup, number theory, graph theory
+- For applied math: connect abstractions to concrete applications`,
+        neuro: `
+NEUROSCIENCE-SPECIFIC GUIDANCE:
+- Specify brain regions using standard atlases (MNI, Talairach coordinates)
+- For neuroimaging: note modality (fMRI, EEG, MEG), preprocessing pipeline
+- Use standard neurotransmitter and receptor nomenclature
+- For behavioral experiments: specify paradigm, n, statistical tests
+- Preferred tools: brain atlas, neurotransmitter lookup, connectome query, EEG analysis
+- Distinguish between correlation and causation in neuroimaging findings`,
+        earth: `
+EARTH SCIENCE-SPECIFIC GUIDANCE:
+- Specify temporal scales (geological time) and spatial scales
+- Use standard geological time periods and epoch names
+- For climate data: note data source, temporal resolution, spatial coverage
+- For seismology: specify magnitude type (Mw, ML), depth, focal mechanism
+- Preferred tools: climate data, earthquake query, ocean data, geological query
+- Always note measurement uncertainties and model limitations`,
+        social: `
+SOCIAL SCIENCE-SPECIFIC GUIDANCE:
+- Report effect sizes alongside p-values
+- Specify methodology: qualitative, quantitative, mixed methods
+- Note sample demographics and potential selection biases
+- For surveys: report response rate, sampling method
+- Preferred tools: statistical analysis, demographic model, survey design, sentiment analysis
+- Distinguish between causal claims and correlational findings
+- Note WEIRD (Western, Educated, Industrialized, Rich, Democratic) sampling biases`,
+        humanities: `
+HUMANITIES-SPECIFIC GUIDANCE:
+- Cite primary sources with full bibliographic detail
+- Distinguish between historical fact, interpretation, and historiographic debate
+- For textual analysis: note edition, translation, original language
+- For philosophical arguments: reconstruct in premise-conclusion form when helpful
+- Preferred tools: archival search, historical timeline, philosophical concepts, corpus analysis
+- Engage with multiple interpretive frameworks rather than privileging one`,
+        health: `
+HEALTH & MEDICINE-SPECIFIC GUIDANCE:
+- Use standard medical terminology (ICD codes, MeSH terms) where appropriate
+- For clinical studies: specify study design (RCT, cohort, case-control), CONSORT/STROBE compliance
+- Note levels of evidence (systematic review > RCT > observational)
+- For drug information: include mechanism of action, pharmacokinetics, contraindications
+- Preferred tools: PubMed search, clinical trials, drug lookup, epidemiology calc
+- Always include appropriate medical disclaimers for clinical information
+- Specify NNT (number needed to treat) and NNH where relevant`,
+        general: `
+GENERAL SCIENCE GUIDANCE:
+- Adapt terminology and rigor to the specific scientific question
+- Cross-reference multiple domains when the question spans fields
+- Use tools from any scientific domain as appropriate
+- Prioritize systematic reviews and meta-analyses for evidence claims`,
+    };
+    // Build variable context if any are set
+    let variableContext = '';
+    const varEntries = Object.entries(session.variables);
+    if (varEntries.length > 0) {
+        variableContext = '\n\nACTIVE VARIABLES:\n' +
+            varEntries.map(([k, v]) => `  ${k} = ${JSON.stringify(v)}`).join('\n') +
+            '\nYou may reference these variables in computations.';
+    }
+    // Build citation context
+    let citationContext = '';
+    if (session.citations.length > 0) {
+        citationContext = '\n\nSESSION CITATIONS:\n' +
+            session.citations.map((c, i) => `  [${i + 1}] ${c.authors.join(', ')} (${c.year}). ${c.title}. ${c.source}${c.doi ? ` DOI: ${c.doi}` : ''}`).join('\n');
+    }
+    return base + domainSpecific[domain] + variableContext + citationContext;
+}
+// ── Storage ──
+function ensureLabDir() {
+    if (!existsSync(LAB_DIR))
+        mkdirSync(LAB_DIR, { recursive: true });
+}
+function sessionPath(id) {
+    return join(LAB_DIR, `${id}.json`);
+}
+function generateSessionId() {
+    const now = new Date();
+    const date = now.toISOString().split('T')[0].replace(/-/g, '');
+    const rand = Math.random().toString(36).slice(2, 6);
+    return `lab-${date}-${rand}`;
+}
+function generateEntryId() {
+    return `e-${Date.now().toString(36)}-${Math.random().toString(36).slice(2, 5)}`;
+}
+function saveLabSession(session) {
+    ensureLabDir();
+    session.lastActiveAt = new Date().toISOString();
+    writeFileSync(sessionPath(session.id), JSON.stringify(session, null, 2));
+}
+function loadLabSession(id) {
+    ensureLabDir();
+    const path = sessionPath(id);
+    if (!existsSync(path))
+        return null;
+    try {
+        return JSON.parse(readFileSync(path, 'utf-8'));
+    }
+    catch {
+        return null;
+    }
+}
+/** List all lab sessions, newest first */
+export function listLabSessions() {
+    ensureLabDir();
+    const files = readdirSync(LAB_DIR).filter(f => f.endsWith('.json'));
+    const sessions = [];
+    for (const file of files) {
+        try {
+            const data = readFileSync(join(LAB_DIR, file), 'utf-8');
+            sessions.push(JSON.parse(data));
+        }
+        catch {
+            continue;
+        }
+    }
+    return sessions.sort((a, b) => new Date(b.lastActiveAt).getTime() - new Date(a.lastActiveAt).getTime());
+}
+/** Get a specific lab session by ID */
+export function getLabSession(id) {
+    return loadLabSession(id);
+}
+/** Prune oldest sessions beyond the limit */
+function pruneLabSessions() {
+    const sessions = listLabSessions();
+    if (sessions.length <= MAX_LAB_SESSIONS)
+        return;
+    const toRemove = sessions.slice(MAX_LAB_SESSIONS);
+    for (const s of toRemove) {
+        const path = sessionPath(s.id);
+        if (existsSync(path))
+            unlinkSync(path);
+    }
+}
+// ── Notebook Management ──
+function addEntry(session, type, content, metadata) {
+    const entry = {
+        id: generateEntryId(),
+        type,
+        content,
+        timestamp: new Date().toISOString(),
+        metadata,
+    };
+    session.notebook.push(entry);
+    return entry;
+}
+function formatNotebook(session) {
+    const domainColor = chalk.hex(DOMAIN_COLORS[session.domain]);
+    const dim = chalk.dim;
+    const lines = [
+        '',
+        domainColor(`  ${DOMAIN_ICONS[session.domain]}  Lab Notebook: ${session.name}`),
+        dim(`  Domain: ${DOMAIN_LABELS[session.domain]}  |  Started: ${new Date(session.startedAt).toLocaleString()}`),
+        dim(`  Entries: ${session.notebook.length}  |  Variables: ${Object.keys(session.variables).length}  |  Citations: ${session.citations.length}`),
+        dim('  ' + '\u2500'.repeat(60)),
+        '',
+    ];
+    if (session.notebook.length === 0) {
+        lines.push(dim('  (empty notebook — start asking questions)'));
+        return lines.join('\n');
+    }
+    const TYPE_BADGES = {
+        query: chalk.hex('#60A5FA')(' Q '),
+        result: chalk.hex('#4ADE80')(' R '),
+        computation: chalk.hex('#FBBF24')(' C '),
+        note: chalk.hex('#67E8F9')(' N '),
+        citation: chalk.hex('#FB923C')(' @ '),
+        hypothesis: chalk.hex('#E879F9')(' H '),
+        figure: chalk.hex('#F472B6')(' F '),
+    };
+    for (const entry of session.notebook) {
+        const badge = TYPE_BADGES[entry.type] || dim(` ${entry.type} `);
+        const time = dim(new Date(entry.timestamp).toLocaleTimeString());
+        const preview = entry.content.length > 120
+            ? entry.content.slice(0, 120) + '...'
+            : entry.content;
+        // For multi-line content, only show first line in overview
+        const firstLine = preview.split('\n')[0];
+        lines.push(`  ${badge} ${time}  ${firstLine}`);
+    }
+    lines.push('');
+    return lines.join('\n');
+}
+// ── Citation Extraction ──
+/** Regex patterns for common citation identifiers */
+const DOI_PATTERN = /\b(10\.\d{4,}\/[^\s,;)\]]+)/g;
+const ARXIV_PATTERN = /\barXiv:(\d{4}\.\d{4,5}(?:v\d+)?)/g;
+const PMID_PATTERN = /\bPMID:?\s*(\d{7,8})/g;
+/** Extract citation references from AI response text */
+function extractCitations(text) {
+    const found = [];
+    const seen = new Set();
+    let match;
+    // DOIs
+    DOI_PATTERN.lastIndex = 0;
+    while ((match = DOI_PATTERN.exec(text)) !== null) {
+        const id = match[1];
+        if (!seen.has(id)) {
+            seen.add(id);
+            found.push({ type: 'doi', id });
+        }
+    }
+    // arXiv IDs
+    ARXIV_PATTERN.lastIndex = 0;
+    while ((match = ARXIV_PATTERN.exec(text)) !== null) {
+        const id = match[1];
+        if (!seen.has(id)) {
+            seen.add(id);
+            found.push({ type: 'arxiv', id });
+        }
+    }
+    // PMIDs
+    PMID_PATTERN.lastIndex = 0;
+    while ((match = PMID_PATTERN.exec(text)) !== null) {
+        const id = match[1];
+        if (!seen.has(id)) {
+            seen.add(id);
+            found.push({ type: 'pmid', id });
+        }
+    }
+    return found;
+}
+/** Convert extracted citation references to Citation objects */
+function refsToStubCitations(refs) {
+    return refs.map(ref => {
+        const citeId = `cite-${Date.now().toString(36)}-${Math.random().toString(36).slice(2, 4)}`;
+        switch (ref.type) {
+            case 'doi':
+                return {
+                    id: citeId,
+                    doi: ref.id,
+                    title: `[DOI: ${ref.id}]`,
+                    authors: [],
+                    year: 0,
+                    source: `https://doi.org/${ref.id}`,
+                };
+            case 'arxiv':
+                return {
+                    id: citeId,
+                    title: `[arXiv: ${ref.id}]`,
+                    authors: [],
+                    year: parseInt(ref.id.slice(0, 2), 10) + 2000,
+                    source: `https://arxiv.org/abs/${ref.id}`,
+                };
+            case 'pmid':
+                return {
+                    id: citeId,
+                    title: `[PMID: ${ref.id}]`,
+                    authors: [],
+                    year: 0,
+                    source: `https://pubmed.ncbi.nlm.nih.gov/${ref.id}/`,
+                };
+        }
+    });
+}
+// ── Variable Extraction ──
+/** Patterns for numeric results that might be worth storing */
+const NUMERIC_RESULT_PATTERNS = [
+    /(?:result|answer|value|equals?|=)\s*[:=]?\s*([-+]?\d+(?:\.\d+)?(?:[eE][-+]?\d+)?)\s*([a-zA-Z/^*]+)?/gi,
+    /(?:approximately|roughly|about|~)\s*([-+]?\d+(?:\.\d+)?(?:[eE][-+]?\d+)?)\s*([a-zA-Z/^*]+)?/gi,
+];
+/** Extract named numeric results from AI response */
+function extractNumericResults(text) {
+    const results = [];
+    // Look for explicit assignments like "F = 9.8 N" or "result: 42.5 km"
+    const assignmentPattern = /\b([A-Za-z_]\w*)\s*[=:]\s*([-+]?\d+(?:\.\d+)?(?:[eE][-+]?\d+)?)\s*([a-zA-Z/^*\u00B0\u00B2\u00B3]+)?/g;
+    let match;
+    assignmentPattern.lastIndex = 0;
+    while ((match = assignmentPattern.exec(text)) !== null) {
+        const name = match[1];
+        const value = parseFloat(match[2]);
+        const unit = match[3];
+        // Skip common false positives
+        const skipNames = new Set(['the', 'and', 'for', 'with', 'from', 'http', 'https', 'www', 'doi', 'ref', 'fig', 'table', 'step', 'line', 'page']);
+        if (skipNames.has(name.toLowerCase()))
+            continue;
+        if (isNaN(value))
+            continue;
+        results.push({ name, value, unit });
+    }
+    return results;
+}
+// ── Export ──
+/** Export the notebook in the requested format */
+export function exportNotebook(session, format = 'markdown') {
+    switch (format) {
+        case 'json':
+            return JSON.stringify({
+                session: {
+                    id: session.id,
+                    name: session.name,
+                    domain: session.domain,
+                    startedAt: session.startedAt,
+                    lastActiveAt: session.lastActiveAt,
+                },
+                notebook: session.notebook,
+                variables: session.variables,
+                citations: session.citations,
+            }, null, 2);
+        case 'latex':
+            return exportAsLatex(session);
+        case 'markdown':
+        default:
+            return exportAsMarkdown(session);
+    }
+}
+function exportAsMarkdown(session) {
+    const lines = [
+        `# Lab Notebook: ${session.name}`,
+        '',
+        `**Domain:** ${DOMAIN_LABELS[session.domain]}`,
+        `**Started:** ${new Date(session.startedAt).toLocaleString()}`,
+        `**Last Active:** ${new Date(session.lastActiveAt).toLocaleString()}`,
+        '',
+        '---',
+        '',
+    ];
+    // Variables section
+    const varEntries = Object.entries(session.variables);
+    if (varEntries.length > 0) {
+        lines.push('## Variables', '');
+        lines.push('| Name | Value |');
+        lines.push('|------|-------|');
+        for (const [name, value] of varEntries) {
+            lines.push(`| \`${name}\` | ${JSON.stringify(value)} |`);
+        }
+        lines.push('');
+    }
+    // Notebook entries
+    lines.push('## Entries', '');
+    for (const entry of session.notebook) {
+        const time = new Date(entry.timestamp).toLocaleString();
+        const typeLabel = entry.type.charAt(0).toUpperCase() + entry.type.slice(1);
+        switch (entry.type) {
+            case 'hypothesis':
+                lines.push(`### Hypothesis (${time})`, '', `> ${entry.content}`, '');
+                break;
+            case 'citation':
+                lines.push(`### Citation (${time})`, '', `- ${entry.content}`, '');
+                break;
+            case 'note':
+                lines.push(`### Note (${time})`, '', entry.content, '');
+                break;
+            case 'query':
+                lines.push(`### Query (${time})`, '', `**Q:** ${entry.content}`, '');
+                break;
+            case 'result':
+                lines.push(`### Result (${time})`, '', entry.content, '');
+                break;
+            case 'computation':
+                lines.push(`### Computation (${time})`, '', '```', entry.content, '```', '');
+                break;
+            case 'figure':
+                lines.push(`### Figure (${time})`, '', entry.content, '');
+                break;
+            default:
+                lines.push(`### ${typeLabel} (${time})`, '', entry.content, '');
+        }
+    }
+    // Citations section
+    if (session.citations.length > 0) {
+        lines.push('## References', '');
+        for (let i = 0; i < session.citations.length; i++) {
+            const c = session.citations[i];
+            const authors = c.authors.length > 0 ? c.authors.join(', ') : 'Unknown';
+            const year = c.year > 0 ? ` (${c.year})` : '';
+            const doi = c.doi ? ` DOI: ${c.doi}` : '';
+            lines.push(`${i + 1}. ${authors}${year}. *${c.title}*. ${c.source}${doi}`);
+        }
+        lines.push('');
+    }
+    return lines.join('\n');
+}
+function exportAsLatex(session) {
+    const lines = [
+        '\\documentclass{article}',
+        '\\usepackage[utf8]{inputenc}',
+        '\\usepackage{amsmath,amssymb}',
+        '\\usepackage{hyperref}',
+        '\\usepackage{booktabs}',
+        '',
+        `\\title{Lab Notebook: ${escapeLatex(session.name)}}`,
+        `\\date{${new Date(session.startedAt).toLocaleDateString()}}`,
+        '',
+        '\\begin{document}',
+        '\\maketitle',
+        '',
+    ];
+    // Variables
+    const varEntries = Object.entries(session.variables);
+    if (varEntries.length > 0) {
+        lines.push('\\section{Variables}', '');
+        lines.push('\\begin{tabular}{ll}', '\\toprule', 'Name & Value \\\\', '\\midrule');
+        for (const [name, value] of varEntries) {
+            lines.push(`\\texttt{${escapeLatex(name)}} & ${escapeLatex(String(value))} \\\\`);
+        }
+        lines.push('\\bottomrule', '\\end{tabular}', '');
+    }
+    // Entries
+    lines.push('\\section{Notebook}', '');
+    for (const entry of session.notebook) {
+        const time = new Date(entry.timestamp).toLocaleString();
+        switch (entry.type) {
+            case 'hypothesis':
+                lines.push(`\\subsection*{Hypothesis (${escapeLatex(time)})}`);
+                lines.push(`\\begin{quote}${escapeLatex(entry.content)}\\end{quote}`);
+                break;
+            case 'query':
+                lines.push(`\\subsection*{Query (${escapeLatex(time)})}`);
+                lines.push(`\\textbf{Q:} ${escapeLatex(entry.content)}`);
+                break;
+            case 'result':
+                lines.push(`\\subsection*{Result (${escapeLatex(time)})}`);
+                lines.push(escapeLatex(entry.content));
+                break;
+            case 'computation':
+                lines.push(`\\subsection*{Computation (${escapeLatex(time)})}`);
+                lines.push('\\begin{verbatim}');
+                lines.push(entry.content);
+                lines.push('\\end{verbatim}');
+                break;
+            default:
+                lines.push(`\\subsection*{${entry.type.charAt(0).toUpperCase() + entry.type.slice(1)} (${escapeLatex(time)})}`);
+                lines.push(escapeLatex(entry.content));
+        }
+        lines.push('');
+    }
+    // References
+    if (session.citations.length > 0) {
+        lines.push('\\section{References}', '', '\\begin{enumerate}');
+        for (const c of session.citations) {
+            const authors = c.authors.length > 0 ? c.authors.join(', ') : 'Unknown';
+            const year = c.year > 0 ? ` (${c.year})` : '';
+            const doi = c.doi ? ` \\texttt{${escapeLatex(c.doi)}}` : '';
+            lines.push(`\\item ${escapeLatex(authors)}${year}. \\textit{${escapeLatex(c.title)}}. ${escapeLatex(c.source)}${doi}`);
+        }
+        lines.push('\\end{enumerate}');
+    }
+    lines.push('', '\\end{document}');
+    return lines.join('\n');
+}
+function escapeLatex(text) {
+    return text
+        .replace(/\\/g, '\\textbackslash{}')
+        .replace(/[&%$#_{}]/g, m => '\\' + m)
+        .replace(/~/g, '\\textasciitilde{}')
+        .replace(/\^/g, '\\textasciicircum{}');
+}
+function parseDOICitation(doiOrUrl) {
+    // Accept bare DOI or full URL
+    const doi = doiOrUrl.replace(/^https?:\/\/doi\.org\//, '').trim();
+    return {
+        id: `cite-${Date.now().toString(36)}-${Math.random().toString(36).slice(2, 4)}`,
+        doi,
+        title: `[DOI: ${doi}]`,
+        authors: [],
+        year: 0,
+        source: `https://doi.org/${doi}`,
+    };
+}
+function handleCommand(input, session) {
+    const trimmed = input.trim();
+    const parts = trimmed.split(/\s+/);
+    const cmd = parts[0].toLowerCase();
+    const rest = trimmed.slice(parts[0].length).trim();
+    switch (cmd) {
+        case '/help':
+            return { continue: true, message: formatHelpText() };
+        case '/domain': {
+            if (!rest) {
+                const domains = Object.keys(DOMAIN_LABELS).map(d => `  ${d === session.domain ? chalk.green('*') : ' '} ${d} — ${DOMAIN_LABELS[d]}`).join('\n');
+                return { continue: true, message: `\nActive domain: ${chalk.bold(DOMAIN_LABELS[session.domain])}\n\n${domains}\n` };
+            }
+            const newDomain = rest.toLowerCase();
+            if (!(newDomain in DOMAIN_LABELS)) {
+                return { continue: true, message: chalk.red(`Unknown domain: ${rest}. Use /domain to see available domains.`) };
+            }
+            session.domain = newDomain;
+            addEntry(session, 'note', `Domain switched to ${DOMAIN_LABELS[newDomain]}`);
+            saveLabSession(session);
+            const color = chalk.hex(DOMAIN_COLORS[newDomain]);
+            return { continue: true, message: color(`\n  ${DOMAIN_ICONS[newDomain]}  Switched to ${DOMAIN_LABELS[newDomain]}\n`) };
+        }
+        case '/notebook':
+            return { continue: true, message: formatNotebook(session) };
+        case '/export': {
+            const fmt = (rest.toLowerCase() || 'markdown');
+            if (!['markdown', 'latex', 'json'].includes(fmt)) {
+                return { continue: true, message: chalk.red('Format must be one of: markdown, latex, json') };
+            }
+            const exported = exportNotebook(session, fmt);
+            const ext = fmt === 'markdown' ? 'md' : fmt === 'latex' ? 'tex' : 'json';
+            const outPath = join(process.cwd(), `${session.id}.${ext}`);
+            try {
+                writeFileSync(outPath, exported);
+                return { continue: true, message: chalk.green(`  Exported to ${outPath}`) };
+            }
+            catch (err) {
+                return { continue: true, message: chalk.red(`Export failed: ${err}`) };
+            }
+        }
+        case '/cite': {
+            if (!rest) {
+                return { continue: true, message: chalk.red('Usage: /cite <doi or url>') };
+            }
+            const citation = parseDOICitation(rest);
+            session.citations.push(citation);
+            addEntry(session, 'citation', `Added citation: ${citation.doi || rest}`);
+            saveLabSession(session);
+            return { continue: true, message: chalk.hex('#FB923C')(`  Added citation: ${citation.doi || rest}`) };
+        }
+        case '/hypothesis': {
+            if (!rest) {
+                return { continue: true, message: chalk.red('Usage: /hypothesis <your hypothesis>') };
+            }
+            addEntry(session, 'hypothesis', rest);
+            saveLabSession(session);
+            return { continue: true, message: chalk.hex('#E879F9')(`  Hypothesis recorded: "${rest.slice(0, 80)}${rest.length > 80 ? '...' : ''}"`) };
+        }
+        case '/note': {
+            if (!rest) {
+                return { continue: true, message: chalk.red('Usage: /note <your note>') };
+            }
+            addEntry(session, 'note', rest);
+            saveLabSession(session);
+            return { continue: true, message: chalk.hex('#67E8F9')(`  Note added.`) };
+        }
+        case '/variables': {
+            const vars = Object.entries(session.variables);
+            if (vars.length === 0) {
+                return { continue: true, message: chalk.dim('  No variables stored. Use /set <name> <value> to store one.') };
+            }
+            const varLines = vars.map(([k, v]) => `  ${chalk.cyan(k)} = ${chalk.white(JSON.stringify(v))}`);
+            return { continue: true, message: `\n  ${chalk.bold('Variables')} (${vars.length})\n${varLines.join('\n')}\n` };
+        }
+        case '/set': {
+            const setParts = rest.split(/\s+/);
+            if (setParts.length < 2) {
+                return { continue: true, message: chalk.red('Usage: /set <name> <value>') };
+            }
+            const varName = setParts[0];
+            const varValueStr = setParts.slice(1).join(' ');
+            // Try to parse as number, then boolean, then keep as string
+            let varValue;
+            const num = Number(varValueStr);
+            if (!isNaN(num) && varValueStr.trim() !== '') {
+                varValue = num;
+            }
+            else if (varValueStr === 'true') {
+                varValue = true;
+            }
+            else if (varValueStr === 'false') {
+                varValue = false;
+            }
+            else {
+                // Try JSON parse for objects/arrays
+                try {
+                    varValue = JSON.parse(varValueStr);
+                }
+                catch {
+                    varValue = varValueStr;
+                }
+            }
+            session.variables[varName] = varValue;
+            saveLabSession(session);
+            return { continue: true, message: chalk.cyan(`  ${varName} = ${JSON.stringify(varValue)}`) };
+        }
+        case '/history': {
+            const sessions = listLabSessions();
+            if (sessions.length === 0) {
+                return { continue: true, message: chalk.dim('  No lab sessions found.') };
+            }
+            const histLines = sessions.slice(0, 20).map(s => {
+                const date = new Date(s.lastActiveAt).toLocaleDateString();
+                const icon = DOMAIN_ICONS[s.domain];
+                const entries = s.notebook.length;
+                const isCurrent = s.id === session.id ? chalk.green(' (current)') : '';
+                return `  ${chalk.dim(s.id)}  ${icon} ${DOMAIN_LABELS[s.domain].padEnd(14)} ${date}  ${entries} entries  "${s.name}"${isCurrent}`;
+            });
+            return { continue: true, message: `\n  ${chalk.bold('Lab Sessions')} (${sessions.length} total)\n\n${histLines.join('\n')}\n` };
+        }
+        case '/resume': {
+            if (!rest) {
+                return { continue: true, message: chalk.red('Usage: /resume <session-id>') };
+            }
+            // Resuming is handled by the main loop — signal intent via metadata
+            return { continue: true, message: `__RESUME__:${rest}` };
+        }
+        case '/clear': {
+            session.notebook = [];
+            session.variables = {};
+            session.citations = [];
+            saveLabSession(session);
+            return { continue: true, message: chalk.dim('  Session cleared.') };
+        }
+        case '/quit':
+        case '/exit':
+        case '/q':
+            return { continue: false, message: undefined };
+        default:
+            return { continue: true, message: chalk.red(`Unknown command: ${cmd}. Type /help for available commands.`) };
+    }
+}
+function formatHelpText() {
+    const h = chalk.hex('#A78BFA');
+    const d = chalk.dim;
+    return `
+  ${h('Lab Commands')}
+
+  ${h('/domain')} ${d('[name]')}       Switch scientific domain (or list domains)
+  ${h('/notebook')}              Show the current session notebook
+  ${h('/export')} ${d('[format]')}     Export notebook (markdown, latex, json)
+  ${h('/cite')} ${d('<doi>')}          Add a citation by DOI
+  ${h('/hypothesis')} ${d('<text>')}   Record a hypothesis
+  ${h('/note')} ${d('<text>')}         Add a research note
+  ${h('/variables')}             Show stored variables
+  ${h('/set')} ${d('<name> <value>')}  Store a variable for reuse
+  ${h('/history')}               List past lab sessions
+  ${h('/resume')} ${d('<id>')}         Resume a previous session
+  ${h('/clear')}                 Clear current session
+  ${h('/help')}                  Show this help
+  ${h('/quit')}                  Exit the lab
+`;
+}
+// ── Lab Banner ──
+function printLabBanner(session) {
+    const domainColor = chalk.hex(DOMAIN_COLORS[session.domain]);
+    const dim = chalk.dim;
+    const banner = `
+${domainColor('  \u250C\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510')}
+${domainColor('  \u2502')}  ${DOMAIN_ICONS[session.domain]}  ${chalk.bold('kbot lab')} ${dim('— Interactive Science REPL')}     ${domainColor('\u2502')}
+${domainColor('  \u2502')}                                                ${domainColor('\u2502')}
+${domainColor('  \u2502')}  Domain:  ${domainColor(DOMAIN_LABELS[session.domain].padEnd(16))}                   ${domainColor('\u2502')}
+${domainColor('  \u2502')}  Session: ${dim(session.name.slice(0, 30).padEnd(30))}           ${domainColor('\u2502')}
+${domainColor('  \u2502')}                                                ${domainColor('\u2502')}
+${domainColor('  \u2502')}  ${dim('Type /help for commands, or ask a question.')}     ${domainColor('\u2502')}
+${domainColor('  \u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518')}
+`;
+    console.error(banner);
+}
+// ── Prompt Builder ──
+function buildLabPrompt(session) {
+    const domainColor = chalk.hex(DOMAIN_COLORS[session.domain]);
+    const dim = chalk.dim;
+    const icon = DOMAIN_ICONS[session.domain];
+    const domainShort = session.domain === 'general' ? 'sci' : session.domain.slice(0, 4);
+    // Status indicators
+    const varCount = Object.keys(session.variables).length;
+    const citeCount = session.citations.length;
+    const statusParts = [];
+    if (varCount > 0)
+        statusParts.push(dim(`${varCount}v`));
+    if (citeCount > 0)
+        statusParts.push(dim(`${citeCount}c`));
+    const status = statusParts.length > 0 ? ` ${dim('[')}${statusParts.join(dim('|'))}${dim(']')}` : '';
+    return `${icon} ${domainColor(`lab:${domainShort}`)}${status}${domainColor('>')} `;
+}
+// ── Main Entry Point ──
+/**
+ * Start the interactive science lab REPL.
+ *
+ * @param opts.domain - Initial scientific domain (default: 'general')
+ * @param opts.resume - Session ID to resume
+ * @param opts.name   - Name for the new session
+ */
+export async function startLab(opts) {
+    const domain = opts?.domain || 'general';
+    let session;
+    // Resume existing session or create new one
+    if (opts?.resume) {
+        const existing = loadLabSession(opts.resume);
+        if (!existing) {
+            // Try fuzzy match
+            const allSessions = listLabSessions();
+            const match = allSessions.find(s => s.id.includes(opts.resume) || s.name.toLowerCase().includes(opts.resume.toLowerCase()));
+            if (match) {
+                session = match;
+                printInfo(`Resumed lab session: ${session.name} (${session.id})`);
+            }
+            else {
+                printError(`Lab session not found: ${opts.resume}`);
+                printInfo('Use /history to see available sessions.');
+                return;
+            }
+        }
+        else {
+            session = existing;
+            printInfo(`Resumed lab session: ${session.name} (${session.id})`);
+        }
+    }
+    else {
+        const id = generateSessionId();
+        const name = opts?.name || `${DOMAIN_LABELS[domain]} Lab — ${new Date().toLocaleDateString()}`;
+        session = {
+            id,
+            name,
+            domain,
+            notebook: [],
+            variables: {},
+            citations: [],
+            startedAt: new Date().toISOString(),
+            lastActiveAt: new Date().toISOString(),
+        };
+        saveLabSession(session);
+    }
+    // Display banner
+    printLabBanner(session);
+    // Gather project context for the agent (non-blocking, best-effort)
+    let projectContext;
+    try {
+        projectContext = await gatherContext();
+    }
+    catch {
+        // Context gathering is optional — lab works without it
+    }
+    // Create readline interface
+    const rl = createInterface({
+        input: process.stdin,
+        output: process.stderr, // Prompt goes to stderr (clig.dev convention)
+        prompt: buildLabPrompt(session),
+        terminal: true,
+    });
+    rl.prompt();
+    // Main REPL loop using event-driven readline
+    const handleLine = async (line) => {
+        const input = line.trim();
+        // Empty input — just re-prompt
+        if (!input) {
+            rl.prompt();
+            return;
+        }
+        // Handle slash commands
+        if (input.startsWith('/')) {
+            const result = handleCommand(input, session);
+            // Handle /resume with session switching
+            if (result.message?.startsWith('__RESUME__:')) {
+                const resumeId = result.message.slice('__RESUME__:'.length);
+                const resumeSession = loadLabSession(resumeId);
+                if (!resumeSession) {
+                    // Fuzzy match
+                    const all = listLabSessions();
+                    const match = all.find(s => s.id.includes(resumeId) || s.name.toLowerCase().includes(resumeId.toLowerCase()));
+                    if (match) {
+                        Object.assign(session, match);
+                        printInfo(`Resumed: ${session.name}`);
+                        printLabBanner(session);
+                    }
+                    else {
+                        console.error(chalk.red(`  Session not found: ${resumeId}`));
+                    }
+                }
+                else {
+                    Object.assign(session, resumeSession);
+                    printInfo(`Resumed: ${session.name}`);
+                    printLabBanner(session);
+                }
+                rl.setPrompt(buildLabPrompt(session));
+                rl.prompt();
+                return;
+            }
+            if (result.message) {
+                console.error(result.message);
+            }
+            if (!result.continue) {
+                rl.close();
+                return;
+            }
+            // Update prompt (domain may have changed)
+            rl.setPrompt(buildLabPrompt(session));
+            rl.prompt();
+            return;
+        }
+        // Regular query — send to the agent
+        // Log the query to the notebook
+        addEntry(session, 'query', input);
+        // Build system prompt with domain context
+        const systemPrompt = buildDomainPrompt(session.domain, session);
+        // Determine the best agent for this domain
+        const agent = DOMAIN_AGENTS[session.domain];
+        // Prepare agent options
+        const agentOpts = {
+            agent,
+            stream: true,
+            context: projectContext,
+        };
+        try {
+            // Show thinking indicator
+            const domainColor = chalk.hex(DOMAIN_COLORS[session.domain]);
+            console.error(domainColor('  ...'));
+            // Wrap the user message with the lab system prompt context
+            const augmentedMessage = `[Lab System Prompt — do not repeat this to the user]\n${systemPrompt}\n[End Lab System Prompt]\n\nUser query: ${input}`;
+            const response = await runAgent(augmentedMessage, agentOpts);
+            // Log the result to the notebook
+            addEntry(session, 'result', response.content, {
+                agent: response.agent,
+                model: response.model,
+                toolCalls: response.toolCalls,
+                tokens: response.usage,
+            });
+            // Auto-extract citations from the response
+            const citationRefs = extractCitations(response.content);
+            if (citationRefs.length > 0) {
+                const newCitations = refsToStubCitations(citationRefs);
+                // Deduplicate against existing citations
+                for (const c of newCitations) {
+                    const alreadyExists = session.citations.some(existing => (existing.doi && c.doi && existing.doi === c.doi) ||
+                        existing.source === c.source);
+                    if (!alreadyExists) {
+                        session.citations.push(c);
+                        addEntry(session, 'citation', `Auto-detected: ${c.doi || c.source}`, { auto: true });
+                    }
+                }
+                if (newCitations.length > 0) {
+                    const newCount = newCitations.filter(c => !session.citations.some(existing => existing.id !== c.id &&
+                        ((existing.doi && c.doi && existing.doi === c.doi) || existing.source === c.source))).length;
+                    if (newCount > 0) {
+                        console.error(chalk.dim(`  [${newCount} citation(s) auto-detected]`));
+                    }
+                }
+            }
+            // Auto-extract and store numeric results
+            const numericResults = extractNumericResults(response.content);
+            let storedVarCount = 0;
+            for (const nr of numericResults) {
+                // Only auto-store if the variable name looks intentional (2+ chars, not common words)
+                if (nr.name.length >= 2 && !session.variables[nr.name]) {
+                    const value = nr.unit ? `${nr.value} ${nr.unit}` : nr.value;
+                    session.variables[nr.name] = value;
+                    storedVarCount++;
+                }
+            }
+            if (storedVarCount > 0) {
+                console.error(chalk.dim(`  [${storedVarCount} variable(s) auto-stored]`));
+            }
+            // Print the response if it wasn't streamed already
+            if (!response.streamed) {
+                console.log();
+                console.log(response.content);
+                console.log();
+            }
+            // Save session state
+            saveLabSession(session);
+        }
+        catch (err) {
+            const errorMsg = err instanceof Error ? err.message : String(err);
+            printError(`Lab agent error: ${errorMsg}`);
+            addEntry(session, 'note', `Error: ${errorMsg}`, { error: true });
+            saveLabSession(session);
+        }
+        // Update prompt and continue
+        rl.setPrompt(buildLabPrompt(session));
+        rl.prompt();
+    };
+    // Wire up the readline events
+    rl.on('line', (line) => {
+        // Pause readline during async processing to avoid prompt duplication
+        rl.pause();
+        handleLine(line).then(() => {
+            rl.resume();
+        }).catch((err) => {
+            printError(`Unexpected error: ${err}`);
+            rl.resume();
+            rl.prompt();
+        });
+    });
+    rl.on('close', () => {
+        // Final save
+        saveLabSession(session);
+        pruneLabSessions();
+        const domainColor = chalk.hex(DOMAIN_COLORS[session.domain]);
+        const entries = session.notebook.length;
+        const vars = Object.keys(session.variables).length;
+        const cites = session.citations.length;
+        console.error('');
+        console.error(domainColor(`  ${DOMAIN_ICONS[session.domain]}  Lab session saved.`));
+        console.error(chalk.dim(`  ID: ${session.id}`));
+        console.error(chalk.dim(`  ${entries} entries, ${vars} variables, ${cites} citations`));
+        console.error(chalk.dim(`  Resume with: kbot lab --resume ${session.id}`));
+        console.error('');
+    });
+    // Handle SIGINT gracefully (Ctrl+C)
+    rl.on('SIGINT', () => {
+        rl.close();
+    });
+    // Return a promise that resolves when the REPL closes
+    return new Promise((resolve) => {
+        rl.on('close', () => resolve());
+    });
+}
+//# sourceMappingURL=lab.js.map