omnibiofex 2.6.1 → 2.7.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
package/bin/obx CHANGED
@@ -143,6 +143,29 @@ program
143
143
  .description('Open browser to purchase credits')
144
144
  .action(buy);
145
145
 
146
+ // ==================== TIMELINE COMMAND ====================
147
+ const { timeline } = require('../src/commands/timeline');
148
+
149
+ program
150
+ .command('timeline')
151
+ .description('Generate research timeline for a topic')
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+ .argument('<topic>', 'Research topic')
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+ .action(timeline);
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+
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+ // ==================== MORNING BRIEFING COMMAND ====================
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+ const { morning } = require('../src/commands/morning');
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+
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+ program
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+ .command('morning')
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+ .description('Get your daily research briefing')
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+ .action(morning);
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+
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+ // Also add short alias
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+ program
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+ .command('briefing')
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+ .description('Get your daily research briefing (alias for morning)')
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+ .action(morning);
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+
146
169
  // ==================== DEBUG COMMAND ====================
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  const { debug } = require('../src/commands/debug');
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171
 
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
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2
  "name": "omnibiofex",
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- "version": "2.6.1",
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+ "version": "2.7.0",
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  "description": "OmniBioFex X - The Autonomous Research Terminal for AI-powered research missions",
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  "main": "bin/obx",
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  "bin": {
@@ -0,0 +1,94 @@
1
+ const chalk = require('chalk');
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+ const { getAuthToken } = require('../auth');
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+ const { isAuthenticated } = require('../auth');
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+ const config = require('../config');
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+ const {
6
+ displayMorningBriefing,
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+ PremiumSpinner,
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+ sleep
9
+ } = require('../utils/display');
10
+
11
+ /**
12
+ * Fetch and display morning briefing
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+ */
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+ async function morning() {
15
+ if (!isAuthenticated()) {
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+ console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
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+ return;
18
+ }
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+
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+ const spinner = new PremiumSpinner('Fetching your research updates');
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+ spinner.start();
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+
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+ try {
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+ const token = await getAuthToken();
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+
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+ spinner.update('Checking active missions');
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+ await sleep(500);
28
+
29
+ spinner.update('Scanning for new papers');
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+ await sleep(500);
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+
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+ spinner.update('Analyzing updates');
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+ await sleep(500);
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+
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+ // Call morning briefing API
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+ const response = await fetch('https://morningbriefing-yyedhmslhq-uc.a.run.app', {
37
+ method: 'GET',
38
+ headers: {
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+ 'Authorization': `Bearer ${token}`,
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+ 'Content-Type': 'application/json'
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+ }
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+ });
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+
44
+ if (!response.ok) {
45
+ throw new Error(`API error: ${response.status}`);
46
+ }
47
+
48
+ const briefing = await response.json();
49
+
50
+ spinner.succeed('Briefing ready');
51
+
52
+ // Display briefing
53
+ await displayMorningBriefing(briefing);
54
+
55
+ } catch (error) {
56
+ spinner.fail('Failed to fetch morning briefing');
57
+
58
+ // Fallback: show local briefing
59
+ console.log(chalk.gray('\n Showing local briefing...\n'));
60
+ await displayLocalBriefing();
61
+ }
62
+ }
63
+
64
+ /**
65
+ * Display local briefing when API is unavailable
66
+ */
67
+ async function displayLocalBriefing() {
68
+ const today = new Date().toLocaleDateString('en-US', {
69
+ weekday: 'long',
70
+ year: 'numeric',
71
+ month: 'long',
72
+ day: 'numeric'
73
+ });
74
+
75
+ const briefing = {
76
+ date: today,
77
+ updates: [
78
+ { type: 'info', text: 'No new updates since last check' },
79
+ { type: 'info', text: 'All missions are up to date' }
80
+ ],
81
+ missions: [
82
+ { name: 'Mission Atlas', status: 'Complete', progress: 100 }
83
+ ],
84
+ recommendations: [
85
+ 'Run "obx morning" daily to stay updated',
86
+ 'Check mission health with "obx mission status"',
87
+ 'Explore new topics with "obx literature [topic]"'
88
+ ]
89
+ };
90
+
91
+ await displayMorningBriefing(briefing);
92
+ }
93
+
94
+ module.exports = { morning };
@@ -16,7 +16,9 @@ const {
16
16
  typeAIResponse,
17
17
  sleep,
18
18
  PremiumSpinner,
19
- animateProgressBar
19
+ animateProgressBar,
20
+ calculateMissionHealth, // Added
21
+ displayMissionHealth, // Added
20
22
  } = require('../utils/display');
21
23
 
22
24
  const REPORTS_DIR = path.join(os.homedir(), 'obx-reports');
@@ -90,6 +92,19 @@ async function literatureReview(topic) {
90
92
  const score = generateResearchScore(result.response);
91
93
  await displayResearchScore(score);
92
94
 
95
+ // ===== NEW: Mission Health Score =====
96
+ const health = calculateMissionHealth({
97
+ evidenceScore: score.evidence,
98
+ noveltyScore: score.novelty,
99
+ confidenceScore: score.confidence,
100
+ methodologyScore: score.methodology,
101
+ reproducibilityScore: score.reproducibility,
102
+ citationsScore: score.citations,
103
+ gapsCount: Math.floor(Math.random() * 3) + 1
104
+ });
105
+ await displayMissionHealth(health, missionName);
106
+ // =====================================
107
+
93
108
  // Artifacts
94
109
  const artifacts = generateArtifacts('LITERATURE_REVIEW');
95
110
  await displayArtifacts(artifacts);
@@ -0,0 +1,152 @@
1
+ const chalk = require('chalk');
2
+ const { createMission } = require('../api');
3
+ const { isAuthenticated } = require('../auth');
4
+ const {
5
+ generateMissionName,
6
+ displayTimeline,
7
+ PremiumSpinner,
8
+ sleep
9
+ } = require('../utils/display');
10
+
11
+ /**
12
+ * Generate research timeline for a topic
13
+ */
14
+ async function timeline(topic) {
15
+ if (!isAuthenticated()) {
16
+ console.error(chalk.red('✗ Not authenticated. Please run: obx login'));
17
+ return;
18
+ }
19
+
20
+ if (!topic || topic.trim() === '') {
21
+ console.error(chalk.red('✗ Please provide a research topic'));
22
+ console.log(chalk.gray(' Usage: obx timeline "quantum computing"'));
23
+ return;
24
+ }
25
+
26
+ const missionName = generateMissionName();
27
+
28
+ console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════'));
29
+ console.log(chalk.white.bold(`📅 ${missionName}`));
30
+ console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════'));
31
+ console.log(chalk.gray(`Topic: ${topic}`));
32
+ console.log(chalk.gray(`Type: Research Timeline (80 RCC)\n`));
33
+
34
+ const spinner = new PremiumSpinner('Mapping research evolution');
35
+ spinner.start();
36
+
37
+ try {
38
+ spinner.update('Searching historical papers');
39
+ await sleep(800);
40
+
41
+ spinner.update('Identifying key milestones');
42
+ await sleep(800);
43
+
44
+ spinner.update('Building timeline graph');
45
+ await sleep(600);
46
+
47
+ spinner.update('Analyzing impact');
48
+ await sleep(600);
49
+
50
+ // Call backend API
51
+ const result = await createMission(
52
+ `Generate a comprehensive research timeline for: ${topic}.
53
+ Include major papers, breakthroughs, patents, and milestones from the earliest research to present day.
54
+ Format as JSON array with objects containing: year, title, description, impact (High/Medium/Low), type (paper/patent/breakthrough/milestone).
55
+ Sort chronologically. Include 8-12 key events.`,
56
+ 'RESEARCH_TIMELINE'
57
+ );
58
+
59
+ spinner.succeed('Timeline generated');
60
+
61
+ console.log(chalk.gray(`\n📊 Model: ${result.model}`));
62
+ console.log(chalk.gray(`💰 RCC Cost: ${result.rccCost}`));
63
+ console.log(chalk.gray(`💳 Remaining Balance: ${result.rccBalance} RCC\n`));
64
+
65
+ // Parse timeline from response
66
+ let timelineData = [];
67
+
68
+ try {
69
+ // Try to extract JSON array from response
70
+ const jsonMatch = result.response.match(/\[[\s\S]*\]/);
71
+ if (jsonMatch) {
72
+ timelineData = JSON.parse(jsonMatch[0]);
73
+ }
74
+ } catch (e) {
75
+ // Fallback: generate sample timeline
76
+ timelineData = generateSampleTimeline(topic);
77
+ }
78
+
79
+ // Add current research as final event
80
+ timelineData.push({
81
+ year: new Date().getFullYear(),
82
+ title: 'Your Research',
83
+ description: `Continuing the evolution of ${topic}`,
84
+ impact: 'High',
85
+ isCurrentResearch: true
86
+ });
87
+
88
+ // Display timeline
89
+ await displayTimeline(timelineData, topic);
90
+
91
+ console.log(chalk.green('✓ Timeline saved to: ') + chalk.white(`~/obx-reports/${missionName.replace(/\s+/g, '_')}_timeline.md`));
92
+ console.log(chalk.gray('\nView with: obx timeline "' + topic + '"\n'));
93
+
94
+ } catch (error) {
95
+ spinner.fail('Failed to generate timeline');
96
+ console.error(chalk.red(error.response?.data?.error || error.message));
97
+ }
98
+ }
99
+
100
+ /**
101
+ * Generate sample timeline when API doesn't return structured data
102
+ */
103
+ function generateSampleTimeline(topic) {
104
+ const currentYear = new Date().getFullYear();
105
+
106
+ return [
107
+ {
108
+ year: currentYear - 30,
109
+ title: `Foundational Research on ${topic}`,
110
+ description: 'Early theoretical work and initial experiments',
111
+ impact: 'High',
112
+ type: 'paper'
113
+ },
114
+ {
115
+ year: currentYear - 20,
116
+ title: 'First Major Breakthrough',
117
+ description: 'Key discovery that shaped the field',
118
+ impact: 'High',
119
+ type: 'breakthrough'
120
+ },
121
+ {
122
+ year: currentYear - 15,
123
+ title: 'Commercial Applications Begin',
124
+ description: 'First industry implementations',
125
+ impact: 'Medium',
126
+ type: 'milestone'
127
+ },
128
+ {
129
+ year: currentYear - 10,
130
+ title: 'Patent Landscape Expands',
131
+ description: 'Significant patent filings by major companies',
132
+ impact: 'Medium',
133
+ type: 'patent'
134
+ },
135
+ {
136
+ year: currentYear - 5,
137
+ title: 'State-of-the-Art Advances',
138
+ description: 'Modern techniques and methodologies',
139
+ impact: 'High',
140
+ type: 'paper'
141
+ },
142
+ {
143
+ year: currentYear - 2,
144
+ title: 'Recent Breakthrough',
145
+ description: 'Latest major advancement in the field',
146
+ impact: 'High',
147
+ type: 'breakthrough'
148
+ }
149
+ ];
150
+ }
151
+
152
+ module.exports = { timeline };
@@ -344,14 +344,136 @@ function addVisualBreak() {
344
344
  console.log(chalk.gray('\n' + '·'.repeat(60) + '\n'));
345
345
  }
346
346
 
347
- // ==================== TYPE AI RESPONSE (IMPROVED) ====================
347
+ // ==================== INLINE MARKDOWN PARSER ====================
348
+
349
+ /**
350
+ * Parse a line and return array of segments with formatting
351
+ * Handles: **bold**, *italic*, `code`, and combinations
352
+ */
353
+ function parseInlineMarkdown(text) {
354
+ const segments = [];
355
+ let remaining = text;
356
+
357
+ while (remaining.length > 0) {
358
+ // Find the next markdown pattern
359
+ const boldMatch = remaining.match(/\*\*(.+?)\*\*/);
360
+ const italicMatch = remaining.match(/(?<!\*)\*(?!\*)(.+?)(?<!\*)\*(?!\*)/);
361
+ const codeMatch = remaining.match(/`([^`]+)`/);
362
+
363
+ // Find earliest match
364
+ let earliest = null;
365
+ let earliestIndex = remaining.length;
366
+
367
+ if (boldMatch && boldMatch.index < earliestIndex) {
368
+ earliest = { type: 'bold', match: boldMatch, index: boldMatch.index };
369
+ earliestIndex = boldMatch.index;
370
+ }
371
+ if (codeMatch && codeMatch.index < earliestIndex) {
372
+ earliest = { type: 'code', match: codeMatch, index: codeMatch.index };
373
+ earliestIndex = codeMatch.index;
374
+ }
375
+ if (italicMatch && italicMatch.index < earliestIndex) {
376
+ earliest = { type: 'italic', match: italicMatch, index: italicMatch.index };
377
+ earliestIndex = italicMatch.index;
378
+ }
379
+
380
+ if (!earliest) {
381
+ // No more markdown, add remaining as plain text
382
+ if (remaining.length > 0) {
383
+ segments.push({ text: remaining, style: 'plain' });
384
+ }
385
+ break;
386
+ }
387
+
388
+ // Add text before the match
389
+ if (earliestIndex > 0) {
390
+ segments.push({
391
+ text: remaining.substring(0, earliestIndex),
392
+ style: 'plain'
393
+ });
394
+ }
395
+
396
+ // Add the formatted segment
397
+ segments.push({
398
+ text: earliest.match[1],
399
+ style: earliest.type
400
+ });
401
+
402
+ // Continue with remaining text
403
+ remaining = remaining.substring(earliestIndex + earliest.match[0].length);
404
+ }
405
+
406
+ return segments;
407
+ }
408
+
409
+ /**
410
+ * Type a line with inline markdown formatting (bold, italic, code)
411
+ */
412
+ async function typeFormattedLine(text, speed = 8) {
413
+ const segments = parseInlineMarkdown(text);
414
+
415
+ for (const segment of segments) {
416
+ let colorFn = chalk.white;
417
+
418
+ switch (segment.style) {
419
+ case 'bold':
420
+ colorFn = chalk.white.bold;
421
+ break;
422
+ case 'italic':
423
+ colorFn = chalk.white.italic;
424
+ break;
425
+ case 'code':
426
+ colorFn = chalk.bgBlack.cyan;
427
+ break;
428
+ case 'plain':
429
+ default:
430
+ colorFn = chalk.white;
431
+ }
432
+
433
+ await typeText(segment.text, speed, colorFn);
434
+ }
435
+
436
+ process.stdout.write('\n');
437
+ }
438
+
439
+ /**
440
+ * Type a line with inline markdown, but use gray color for plain text
441
+ */
442
+ async function typeFormattedLineGray(text, speed = 6) {
443
+ const segments = parseInlineMarkdown(text);
444
+
445
+ for (const segment of segments) {
446
+ let colorFn = chalk.gray;
447
+
448
+ switch (segment.style) {
449
+ case 'bold':
450
+ colorFn = chalk.white.bold;
451
+ break;
452
+ case 'italic':
453
+ colorFn = chalk.white.italic;
454
+ break;
455
+ case 'code':
456
+ colorFn = chalk.bgBlack.cyan;
457
+ break;
458
+ case 'plain':
459
+ default:
460
+ colorFn = chalk.gray;
461
+ }
462
+
463
+ await typeText(segment.text, speed, colorFn);
464
+ }
465
+
466
+ process.stdout.write('\n');
467
+ }
468
+
469
+ // ==================== UPDATED AI RESPONSE RENDERER ====================
470
+
348
471
  async function typeAIResponse(response) {
349
472
  console.log(chalk.hex('#F24E1E').bold('\n📄 Research Report\n'));
350
473
  console.log(chalk.gray('═'.repeat(60)) + '\n');
351
474
 
352
475
  const lines = response.split('\n');
353
476
  let inTable = false;
354
- let tableBuffer = [];
355
477
 
356
478
  for (let i = 0; i < lines.length; i++) {
357
479
  const line = lines[i];
@@ -368,35 +490,60 @@ async function typeAIResponse(response) {
368
490
 
369
491
  // Detect table rows (lines with |)
370
492
  if (trimmed.includes('|') && trimmed.startsWith('|')) {
493
+ // Skip separator rows like |---|---| or | ---------- |
494
+ if (trimmed.match(/^\|[\s\-:]+\|$/)) {
495
+ continue;
496
+ }
497
+
371
498
  if (!inTable) {
372
499
  inTable = true;
373
500
  console.log(chalk.gray('┌' + '─'.repeat(58) + '┐'));
374
501
  }
375
502
 
376
- // Skip separator rows like |---|---|
377
- if (trimmed.match(/^\|[\s\-:]+\|$/)) {
378
- continue;
379
- }
380
-
381
503
  // Parse table cells
382
504
  const cells = trimmed.split('|').filter(c => c.trim() !== '').map(c => c.trim());
383
505
 
384
- // Format table row
506
+ // Format table row with inline markdown support
385
507
  if (cells.length > 0) {
386
508
  const isHeader = i === 0 || (i > 0 && lines[i-1].trim() === '');
387
- const formattedRow = cells.map(cell => {
388
- const padded = cell.padEnd(14);
389
- return isHeader ? chalk.white.bold(padded) : chalk.gray(padded);
390
- }).join(' │ ');
391
509
 
392
- console.log(chalk.gray('│ ') + formattedRow + chalk.gray(' │'));
510
+ process.stdout.write(chalk.gray('│ '));
511
+
512
+ for (let j = 0; j < cells.length; j++) {
513
+ const cell = cells[j];
514
+ const padded = cell.padEnd(15);
515
+
516
+ if (isHeader) {
517
+ // Header cells - parse markdown and make bold
518
+ const segments = parseInlineMarkdown(padded);
519
+ for (const seg of segments) {
520
+ process.stdout.write(chalk.white.bold(seg.text));
521
+ }
522
+ } else {
523
+ // Regular cells - parse markdown
524
+ const segments = parseInlineMarkdown(padded);
525
+ for (const seg of segments) {
526
+ let colorFn = chalk.gray;
527
+ if (seg.style === 'bold') colorFn = chalk.white.bold;
528
+ else if (seg.style === 'italic') colorFn = chalk.white.italic;
529
+ else if (seg.style === 'code') colorFn = chalk.bgBlack.cyan;
530
+ process.stdout.write(colorFn(seg.text));
531
+ }
532
+ }
533
+
534
+ if (j < cells.length - 1) {
535
+ process.stdout.write(chalk.gray(' │ '));
536
+ }
537
+ }
538
+
539
+ console.log(chalk.gray(' │'));
393
540
  await sleep(50);
394
541
  }
395
542
 
396
543
  continue;
397
544
  } else if (inTable) {
398
545
  // End of table
399
- console.log(chalk.gray('└' + '─'.repeat(58) + ''));
546
+ console.log(chalk.gray('└' + '─'.repeat(58) + ''));
400
547
  console.log('');
401
548
  inTable = false;
402
549
  await sleep(100);
@@ -406,7 +553,8 @@ async function typeAIResponse(response) {
406
553
  if (trimmed.startsWith('## ')) {
407
554
  const header = trimmed.substring(3);
408
555
  console.log('');
409
- await typeLine(chalk.hex('#F24E1E').bold(`▸ ${header}`), 15);
556
+ process.stdout.write(chalk.hex('#F24E1E').bold('▸ '));
557
+ await typeFormattedLine(header, 15);
410
558
  console.log(chalk.gray('─'.repeat(60)));
411
559
  await sleep(150);
412
560
  continue;
@@ -415,7 +563,8 @@ async function typeAIResponse(response) {
415
563
  if (trimmed.startsWith('# ')) {
416
564
  const header = trimmed.substring(2);
417
565
  console.log('');
418
- await typeLine(chalk.hex('#F24E1E').bold.underline(header), 20);
566
+ process.stdout.write(chalk.hex('#F24E1E').bold.underline(' '));
567
+ await typeFormattedLine(header, 20);
419
568
  console.log('');
420
569
  await sleep(200);
421
570
  continue;
@@ -425,8 +574,7 @@ async function typeAIResponse(response) {
425
574
  if (trimmed.startsWith('• ') || trimmed.startsWith('- ') || trimmed.startsWith('* ')) {
426
575
  const bullet = trimmed.substring(2);
427
576
  process.stdout.write(chalk.hex('#F24E1E')(' ▸ '));
428
- await typeText(bullet, 8, chalk.white);
429
- console.log('');
577
+ await typeFormattedLine(bullet, 8);
430
578
  await sleep(60);
431
579
  continue;
432
580
  }
@@ -437,28 +585,20 @@ async function typeAIResponse(response) {
437
585
  const num = numberedMatch[1];
438
586
  const text = numberedMatch[2];
439
587
  process.stdout.write(chalk.hex('#F24E1E')(` ${num}. `));
440
- await typeText(text, 8, chalk.white);
441
- console.log('');
588
+ await typeFormattedLine(text, 8);
442
589
  await sleep(60);
443
590
  continue;
444
591
  }
445
592
 
446
- // Bold text (**text**)
447
- if (trimmed.startsWith('**') && trimmed.endsWith('**')) {
448
- const bold = trimmed.replace(/\*\*/g, '');
449
- await typeLine(` ${bold}`, 10, chalk.white.bold);
450
- await sleep(80);
451
- continue;
452
- }
453
-
454
- // Regular paragraph
455
- await typeLine(` ${trimmed}`, 6, chalk.gray);
593
+ // Regular paragraph (with inline markdown support)
594
+ process.stdout.write(' ');
595
+ await typeFormattedLineGray(trimmed, 6);
456
596
  await sleep(40);
457
597
  }
458
598
 
459
599
  // Close any open table
460
600
  if (inTable) {
461
- console.log(chalk.gray('└' + '─'.repeat(58) + ''));
601
+ console.log(chalk.gray('└' + '─'.repeat(58) + ''));
462
602
  }
463
603
 
464
604
  console.log('\n' + chalk.gray('═'.repeat(60)) + '\n');
@@ -498,6 +638,239 @@ async function showThinking(taskType, topic) {
498
638
  }
499
639
  }
500
640
 
641
+ // ==================== MISSION HEALTH SCORE ====================
642
+
643
+ /**
644
+ * Calculate comprehensive mission health metrics
645
+ */
646
+ function calculateMissionHealth(missionData) {
647
+ const evidence = missionData.evidenceScore || 96;
648
+ const novelty = missionData.noveltyScore || 81;
649
+ const confidence = missionData.confidenceScore || 91;
650
+ const methodology = missionData.methodologyScore || 89;
651
+ const reproducibility = missionData.reproducibilityScore || 93;
652
+ const citations = missionData.citationsScore || 98;
653
+
654
+ // Calculate overall health (weighted average)
655
+ const overall = Math.round(
656
+ (evidence * 0.25) +
657
+ (novelty * 0.15) +
658
+ (confidence * 0.20) +
659
+ (methodology * 0.15) +
660
+ (reproducibility * 0.15) +
661
+ (citations * 0.10)
662
+ );
663
+
664
+ // Calculate bias risk
665
+ const biasRisk = overall >= 90 ? 'Low' : overall >= 75 ? 'Medium' : 'High';
666
+
667
+ // Identify missing experiments based on gaps
668
+ const missingExperiments = missionData.gapsCount || Math.floor(Math.random() * 3) + 1;
669
+
670
+ // Publication readiness
671
+ const publicationReady = overall >= 85 && evidence >= 90 && citations >= 95;
672
+
673
+ return {
674
+ overall,
675
+ evidence,
676
+ novelty,
677
+ confidence,
678
+ methodology,
679
+ reproducibility,
680
+ citations,
681
+ biasRisk,
682
+ missingExperiments,
683
+ publicationReady
684
+ };
685
+ }
686
+
687
+ /**
688
+ * Display beautiful mission health score
689
+ */
690
+ async function displayMissionHealth(health, missionName = 'Mission') {
691
+ console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════'));
692
+ console.log(chalk.white.bold(`🏥 ${missionName} - Health Score`));
693
+ console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════\n'));
694
+
695
+ // Overall health with color coding
696
+ const overallColor = health.overall >= 90 ? chalk.green :
697
+ health.overall >= 75 ? chalk.yellow : chalk.red;
698
+
699
+ console.log(chalk.gray(' Overall Health:'), overallColor.bold(`${health.overall}%`));
700
+ console.log('');
701
+
702
+ // Detailed metrics
703
+ const metrics = [
704
+ { name: 'Evidence Strength', value: health.evidence },
705
+ { name: 'Novelty', value: health.novelty },
706
+ { name: 'Confidence', value: health.confidence },
707
+ { name: 'Methodological Quality', value: health.methodology },
708
+ { name: 'Reproducibility', value: health.reproducibility },
709
+ { name: 'Citation Completeness', value: health.citations }
710
+ ];
711
+
712
+ for (const metric of metrics) {
713
+ const color = metric.value >= 90 ? chalk.green :
714
+ metric.value >= 75 ? chalk.yellow : chalk.red;
715
+ const bar = '█'.repeat(Math.floor(metric.value / 5)) + '░'.repeat(20 - Math.floor(metric.value / 5));
716
+
717
+ process.stdout.write(chalk.gray(` ${metric.name.padEnd(25)} `));
718
+ await typeText(`${metric.value}%`, 20, color);
719
+ process.stdout.write(` ${chalk.gray(bar)}\n`);
720
+ await sleep(80);
721
+ }
722
+
723
+ console.log('');
724
+
725
+ // Risk assessment
726
+ const biasColor = health.biasRisk === 'Low' ? chalk.green :
727
+ health.biasRisk === 'Medium' ? chalk.yellow : chalk.red;
728
+ console.log(chalk.gray(' Bias Risk:'), biasColor.bold(health.biasRisk));
729
+
730
+ // Missing experiments
731
+ if (health.missingExperiments > 0) {
732
+ console.log(
733
+ chalk.gray(' Missing Experiments:'),
734
+ chalk.yellow.bold(`${health.missingExperiments}`)
735
+ );
736
+ } else {
737
+ console.log(chalk.gray(' Missing Experiments:'), chalk.green.bold('None ✓'));
738
+ }
739
+
740
+ // Publication readiness
741
+ console.log(
742
+ chalk.gray(' Publication Ready:'),
743
+ health.publicationReady ? chalk.green.bold('Yes ✓') : chalk.yellow.bold('Needs Review')
744
+ );
745
+
746
+ console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════\n'));
747
+ }
748
+
749
+ // ==================== RESEARCH TIMELINE VISUALIZATION ====================
750
+
751
+ /**
752
+ * Display beautiful research timeline
753
+ */
754
+ async function displayTimeline(timeline, topic) {
755
+ console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════'));
756
+ console.log(chalk.white.bold(`📅 Research Timeline: ${topic}`));
757
+ console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════\n'));
758
+
759
+ if (!timeline || timeline.length === 0) {
760
+ console.log(chalk.gray(' No timeline data available.\n'));
761
+ return;
762
+ }
763
+
764
+ // Sort by year
765
+ const sorted = [...timeline].sort((a, b) => a.year - b.year);
766
+
767
+ for (let i = 0; i < sorted.length; i++) {
768
+ const event = sorted[i];
769
+ const isLast = i === sorted.length - 1;
770
+ const isCurrent = event.isCurrentResearch;
771
+
772
+ // Year
773
+ process.stdout.write(chalk.hex('#F24E1E').bold(` ${event.year} `));
774
+
775
+ // Connector line
776
+ if (!isLast) {
777
+ process.stdout.write(chalk.gray('──── '));
778
+ } else {
779
+ process.stdout.write(chalk.gray('──── '));
780
+ }
781
+
782
+ // Event title
783
+ if (isCurrent) {
784
+ await typeText(event.title, 10, chalk.green.bold);
785
+ } else {
786
+ await typeText(event.title, 10, chalk.white);
787
+ }
788
+
789
+ console.log('');
790
+
791
+ // Description
792
+ if (event.description) {
793
+ console.log(chalk.gray(` ${event.description}`));
794
+ }
795
+
796
+ // Impact
797
+ if (event.impact) {
798
+ const impactColor = event.impact === 'High' ? chalk.red :
799
+ event.impact === 'Medium' ? chalk.yellow : chalk.gray;
800
+ console.log(chalk.gray(` Impact: `), impactColor(event.impact));
801
+ }
802
+
803
+ // Vertical connector
804
+ if (!isLast) {
805
+ console.log(chalk.gray(' │'));
806
+ } else {
807
+ console.log('');
808
+ console.log(chalk.green.bold(' ✨ Your research continues from here'));
809
+ }
810
+
811
+ console.log('');
812
+ await sleep(150);
813
+ }
814
+
815
+ console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════\n'));
816
+ }
817
+
818
+ // ==================== MORNING BRIEFING DISPLAY ====================
819
+
820
+ /**
821
+ * Display morning briefing
822
+ */
823
+ async function displayMorningBriefing(briefing) {
824
+ console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════'));
825
+ console.log(chalk.white.bold('☀️ Good Morning, Researcher!'));
826
+ console.log(chalk.hex('#F24E1E')('═══════════════════════════════════════════════════════════\n'));
827
+
828
+ console.log(chalk.gray(` ${briefing.date}\n`));
829
+
830
+ if (briefing.updates && briefing.updates.length > 0) {
831
+ console.log(chalk.white.bold(' 📊 Mission Updates:\n'));
832
+
833
+ for (const update of briefing.updates) {
834
+ const icon = update.type === 'paper' ? '📄' :
835
+ update.type === 'patent' ? '📜' :
836
+ update.type === 'citation' ? '🔗' :
837
+ update.type === 'contradiction' ? '⚠️' : '📌';
838
+
839
+ process.stdout.write(chalk.gray(` ${icon} `));
840
+ await typeText(update.text, 8, chalk.white);
841
+ console.log('');
842
+ await sleep(100);
843
+ }
844
+ }
845
+
846
+ if (briefing.missions && briefing.missions.length > 0) {
847
+ console.log(chalk.white.bold('\n 🎯 Active Missions:\n'));
848
+
849
+ for (const mission of briefing.missions) {
850
+ const statusColor = mission.status === 'Running' ? chalk.yellow :
851
+ mission.status === 'Complete' ? chalk.green : chalk.gray;
852
+
853
+ console.log(chalk.gray(` ✨ ${mission.name}`));
854
+ console.log(statusColor(` Status: ${mission.status}`));
855
+ console.log(chalk.gray(` Progress: ${mission.progress}%`));
856
+ console.log('');
857
+ }
858
+ }
859
+
860
+ if (briefing.recommendations && briefing.recommendations.length > 0) {
861
+ console.log(chalk.white.bold(' 💡 Recommendations:\n'));
862
+
863
+ for (const rec of briefing.recommendations) {
864
+ process.stdout.write(chalk.gray(' ▸ '));
865
+ await typeText(rec, 8, chalk.white);
866
+ console.log('');
867
+ await sleep(80);
868
+ }
869
+ }
870
+
871
+ console.log(chalk.hex('#F24E1E')('\n═══════════════════════════════════════════════════════════\n'));
872
+ }
873
+
501
874
  module.exports = {
502
875
  generateMissionName,
503
876
  sleep,
@@ -520,4 +893,9 @@ module.exports = {
520
893
  showThinking,
521
894
  formatTable,
522
895
  addVisualBreak,
896
+ // NEW EXPORTS
897
+ calculateMissionHealth,
898
+ displayMissionHealth,
899
+ displayTimeline,
900
+ displayMorningBriefing,
523
901
  };