Add manuscript unit consistency assistant

manuscript-unit-consistency-assistant/README.md

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+# Manuscript Unit Consistency Assistant
+
+Dependency-free AI peer-review aid slice for SCIBASE issue #13.
+
+This module audits draft manuscript packets for unit hygiene risks that slow down scientific peer review:
+
+- numeric values that appear without adjacent units
+- the same reagent or outcome reported across incompatible unit families
+- table header units that drift from cell-level units
+- implausible wet-lab temperature or percentage values
+- reviewer-ready actions and deterministic audit digests
+
+The implementation uses synthetic sample data only. It is designed as a small, auditable MVP component that can sit behind an AI-assisted pre-submission review workflow.
+
+## Run
+
+```bash
+npm --prefix manuscript-unit-consistency-assistant run check
+npm --prefix manuscript-unit-consistency-assistant test
+npm --prefix manuscript-unit-consistency-assistant run demo
+
+node manuscript-unit-consistency-assistant/test.js
+node manuscript-unit-consistency-assistant/demo.js
+node --check manuscript-unit-consistency-assistant/index.js
+node --check manuscript-unit-consistency-assistant/sample-data.js
+node --check manuscript-unit-consistency-assistant/test.js
+node --check manuscript-unit-consistency-assistant/demo.js
+```
+
+The demo writes:
+
+- `reports/unit-consistency-report.json`
+- `reports/unit-consistency-report.md`
+- `reports/unit-consistency-summary.svg`
+- `reports/demo-script.txt`
+- `reports/demo.mp4`
+
+## API
+
+```js
+const { analyzeManuscript } = require("./index");
+
+const result = analyzeManuscript({
+  manuscriptId: "draft-001",
+  title: "Draft title",
+  trackedTerms: [{ name: "IL-6", aliases: ["IL-6", "IL6"] }],
+  sections: [{ id: "methods", title: "Methods", text: "IL-6 was measured at 180 pg/mL." }],
+  tables: [],
+});
+```
+
+`result` contains a readiness summary, findings, reviewer actions, measurement inventory, and a stable audit digest.

manuscript-unit-consistency-assistant/acceptance-notes.md

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+# Acceptance Notes
+
+## What Changed
+
+- Added a self-contained manuscript unit consistency assistant.
+- Added synthetic sample data that demonstrates missing units, molar-vs-mass concentration conflicts, table unit drift, and implausible temperature detection.
+- Added deterministic tests and demo artifacts for local review.
+
+## Verification Targets
+
+- The module runs with Node.js and no third-party dependencies.
+- Findings include stable IDs, evidence snippets, recommendations, and severity.
+- Reports are deterministic across repeated runs.
+- Clean sample manuscripts return a 100 readiness score with no findings.
+- The included demo video is H.264, 1280x720, and 4 seconds long.
+
+## Local Validation
+
+```bash
+npm --prefix manuscript-unit-consistency-assistant run check
+npm --prefix manuscript-unit-consistency-assistant test
+npm --prefix manuscript-unit-consistency-assistant run demo
+node manuscript-unit-consistency-assistant/test.js
+node manuscript-unit-consistency-assistant/demo.js
+node --check manuscript-unit-consistency-assistant/index.js
+node --check manuscript-unit-consistency-assistant/sample-data.js
+node --check manuscript-unit-consistency-assistant/test.js
+node --check manuscript-unit-consistency-assistant/demo.js
+git diff --check
+mdls -name kMDItemDurationSeconds -name kMDItemCodecs -name kMDItemPixelHeight -name kMDItemPixelWidth manuscript-unit-consistency-assistant/reports/demo.mp4
+```

manuscript-unit-consistency-assistant/demo.js

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+"use strict";
+
+const fs = require("node:fs");
+const path = require("node:path");
+const { analyzeManuscript } = require("./index");
+const { sampleManuscript } = require("./sample-data");
+
+const outputDir = path.join(__dirname, "reports");
+const report = analyzeManuscript(sampleManuscript);
+
+fs.mkdirSync(outputDir, { recursive: true });
+fs.writeFileSync(
+  path.join(outputDir, "unit-consistency-report.json"),
+  `${JSON.stringify(report, null, 2)}\n`
+);
+fs.writeFileSync(
+  path.join(outputDir, "unit-consistency-report.md"),
+  renderMarkdown(report)
+);
+fs.writeFileSync(
+  path.join(outputDir, "unit-consistency-summary.svg"),
+  renderSvg(report)
+);
+fs.writeFileSync(
+  path.join(outputDir, "demo-script.txt"),
+  renderDemoScript(report)
+);
+
+console.log(`Wrote reports to ${outputDir}`);
+
+function renderMarkdown(result) {
+  const lines = [
+    "# Manuscript Unit Consistency Report",
+    "",
+    `Manuscript: ${result.summary.title}`,
+    `Audit digest: ${result.auditDigest}`,
+    `Readiness: ${result.summary.readiness} (${result.summary.readinessScore}/100)`,
+    "",
+    "## Findings",
+    "",
+  ];
+
+  if (result.findings.length === 0) {
+    lines.push("No unit consistency findings were detected.");
+  } else {
+    result.findings.forEach((finding) => {
+      lines.push(`- ${finding.severity.toUpperCase()} ${finding.type}: ${finding.message}`);
+      lines.push(`  Evidence: ${finding.evidence}`);
+      lines.push(`  Action: ${finding.recommendation}`);
+    });
+  }
+
+  lines.push("", "## Reviewer Actions", "");
+  result.reviewerActions.forEach((action) => {
+    lines.push(`- P${action.priority} ${action.action} (${action.sourceId})`);
+  });
+
+  lines.push("", "## Measurement Inventory", "");
+  result.measurementInventory.forEach((measurement) => {
+    lines.push(`- ${measurement.sourceId}: ${measurement.raw} -> ${measurement.unitFamily} (${measurement.subject || "untracked"})`);
+  });
+
+  return `${lines.join("\n")}\n`;
+}
+
+function renderDemoScript(result) {
+  return [
+    "Demo storyboard for manuscript-unit-consistency-assistant",
+    "",
+    "1. Load a draft manuscript packet with sections, tables, and tracked terms.",
+    `2. Extract ${result.summary.measurementsReviewed} measurements from methods, results, and table cells.`,
+    `3. Surface ${result.findings.length} reviewer findings, prioritizing high-severity blockers first.`,
+    "4. Export JSON, Markdown, and SVG artifacts for an AI peer-review aid workflow.",
+    "",
+    `Readiness result: ${result.summary.readiness} (${result.summary.readinessScore}/100).`,
+    `Audit digest: ${result.auditDigest}.`,
+    "",
+  ].join("\n");
+}
+
+function renderSvg(result) {
+  const high = result.summary.findingsBySeverity.high || 0;
+  const medium = result.summary.findingsBySeverity.medium || 0;
+  const low = result.summary.findingsBySeverity.low || 0;
+  const score = result.summary.readinessScore;
+  const bars = [
+    { label: "High", value: high, color: "#d92d20", y: 150 },
+    { label: "Medium", value: medium, color: "#f79009", y: 205 },
+    { label: "Low", value: low, color: "#475467", y: 260 },
+  ];
+  const max = Math.max(1, high, medium, low);
+  const barSvg = bars.map((bar) => {
+    const width = 360 * (bar.value / max);
+    return [
+      `<text x="42" y="${bar.y - 8}" font-family="Arial" font-size="17" fill="#101828">${bar.label}: ${bar.value}</text>`,
+      `<rect x="42" y="${bar.y}" width="${Math.max(8, width)}" height="26" rx="4" fill="${bar.color}"/>`,
+    ].join("\n");
+  }).join("\n");
+
+  return [
+    '<svg xmlns="http://www.w3.org/2000/svg" width="920" height="420" viewBox="0 0 920 420">',
+    '<rect width="920" height="420" fill="#f8fafc"/>',
+    '<rect x="24" y="24" width="872" height="372" rx="8" fill="#ffffff" stroke="#d0d5dd"/>',
+    '<text x="42" y="72" font-family="Arial" font-size="30" font-weight="700" fill="#101828">Manuscript Unit Consistency Assistant</text>',
+    `<text x="42" y="110" font-family="Arial" font-size="18" fill="#475467">${escapeXml(result.summary.title)}</text>`,
+    `<text x="42" y="135" font-family="Arial" font-size="15" fill="#667085">Audit digest ${result.auditDigest}</text>`,
+    barSvg,
+    `<circle cx="730" cy="205" r="86" fill="#ecfdf3" stroke="#12b76a" stroke-width="10"/>`,
+    `<text x="730" y="195" font-family="Arial" font-size="42" font-weight="700" text-anchor="middle" fill="#027a48">${score}</text>`,
+    '<text x="730" y="228" font-family="Arial" font-size="16" text-anchor="middle" fill="#027a48">readiness score</text>',
+    `<text x="730" y="286" font-family="Arial" font-size="17" text-anchor="middle" fill="#344054">${escapeXml(result.summary.readiness)}</text>`,
+    '</svg>',
+    "",
+  ].join("\n");
+}
+
+function escapeXml(value) {
+  return String(value)
+    .replace(/&/g, "&amp;")
+    .replace(/</g, "&lt;")
+    .replace(/>/g, "&gt;")
+    .replace(/"/g, "&quot;");
+}