# Hypothesis Generation Skill - Fix Complete ✅

## Problem

When requesting hypothesis generation documents, the system was creating generic LaTeX papers instead of the specialized colored-box format designed specifically for hypothesis generation reports.

## Solution

Fixed the hypothesis generation skill to properly use its specialized template with colored boxes, comprehensive appendices, and professional formatting.

## What Was Fixed

### 1. **Added Missing Template Files** ✅

The hypothesis-generation skill was missing critical LaTeX files:

**Files Added:**
- `hypothesis_generation.sty` - Custom style package with colored box environments
- `hypothesis_report_template.tex` - Complete structured template
- `FORMATTING_GUIDE.md` - Quick reference guide

**Locations Updated:**
- `scientific_writer/.claude/skills/hypothesis-generation/assets/` (package)
- `.claude/skills/hypothesis-generation/assets/` (workspace)

### 2. **Added Detection Logic to WRITER.md** ✅

Updated system instructions to automatically detect and handle hypothesis generation requests.

**Detection Keywords:**
- "hypothesis generation"
- "generate hypotheses"
- "competing hypotheses"
- "testable hypotheses"
- "mechanistic hypotheses"

### 3. **Proper Template Structure** ✅

The template now includes:

**Colored Hypothesis Boxes:**
- `hypothesisbox1` (Deep Blue)
- `hypothesisbox2` (Forest Green)
- `hypothesisbox3` (Royal Purple)
- `hypothesisbox4` (Teal)
- `hypothesisbox5` (Burnt Orange)

**Utility Boxes:**
- `summarybox` (Executive Summary)
- `predictionbox` (Testable Predictions)
- `comparisonbox` (Critical Comparisons)
- `evidencebox` (Supporting Evidence)
- `limitationbox` (Limitations)

**Document Structure:**
- **Main Text (4 pages max):**
  - Executive Summary (0.5-1 page)
  - Competing Hypotheses (2-2.5 pages)
  - Testable Predictions (0.5-1 page)
  - Critical Comparisons (0.5-1 page)

- **Appendices (Comprehensive):**
  - Appendix A: Comprehensive Literature Review
  - Appendix B: Detailed Experimental Designs
  - Appendix C: Quality Assessment Tables
  - Appendix D: Supplementary Evidence

### 4. **Correct Compilation** ✅

Now uses **XeLaTeX** (not pdflatex) for proper rendering:

```bash
xelatex hypothesis_report.tex
bibtex hypothesis_report
xelatex hypothesis_report.tex
xelatex hypothesis_report.tex
```

## Expected Behavior Now

When you request hypothesis generation, the system will:

1. **Detect** the request automatically
2. **Print** detection messages:
   ```
   [HH:MM:SS] DETECTED: Hypothesis generation document requested
   [HH:MM:SS] FORMAT: Using colored-box LaTeX template
   [HH:MM:SS] COMPILER: XeLaTeX required for proper rendering
   [HH:MM:SS] STRUCTURE: 4-page main text + comprehensive appendices
   ```
3. **Use** the proper colored-box template
4. **Generate** 3-5 competing hypotheses in colored boxes
5. **Include** comprehensive appendices with 50+ citations
6. **Compile** with XeLaTeX for professional output

## Example Usage

```
"Create a new hypothesis generation document for how AI can be used 
to predict age using gene expression data from ARCHS4"
```

**Result:**
- ✅ Professional colored boxes for each hypothesis
- ✅ 4-page concise main text
- ✅ Comprehensive appendices with extensive literature review
- ✅ Detailed experimental designs
- ✅ Quality assessment tables
- ✅ 50+ real citations from research-lookup
- ✅ Beautiful PDF with proper formatting

## Before vs After

### Before (Broken) ❌
- Generic LaTeX article format
- No colored boxes
- No structured appendices
- Compiled with pdflatex
- Missing visual organization
- Single continuous document

### After (Fixed) ✅
- Specialized hypothesis generation template
- Color-coded hypothesis boxes (5 colors)
- Comprehensive structured appendices
- Compiled with XeLaTeX
- Professional visual organization
- 4-page concise main text + detailed appendices

## Files Modified

1. **Added to package:**
   - `scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_generation.sty`
   - `scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_report_template.tex`
   - `scientific_writer/.claude/skills/hypothesis-generation/assets/FORMATTING_GUIDE.md`

2. **Added to workspace:**
   - `.claude/skills/hypothesis-generation/assets/hypothesis_generation.sty`
   - `.claude/skills/hypothesis-generation/assets/hypothesis_report_template.tex`
   - `.claude/skills/hypothesis-generation/assets/FORMATTING_GUIDE.md`

3. **Updated instructions:**
   - `templates/CLAUDE.scientific-writer.md` (template)
   - `scientific_writer/.claude/WRITER.md` (package)
   - `.claude/WRITER.md` (workspace)

## Verification

All components verified:
- ✅ Template files in place
- ✅ Style package in place
- ✅ Formatting guide in place
- ✅ WRITER.md updated with detection logic
- ✅ Both package and workspace updated
- ✅ XeLaTeX compilation instructions clear

## Status

**✅ FIX COMPLETE AND READY TO USE**

The hypothesis generation skill will now work correctly. Just request "hypothesis generation" and the system will automatically:
1. Detect it's a hypothesis generation request
2. Use the proper colored-box template
3. Follow the specialized workflow
4. Generate a professional hypothesis report

---

**Date Fixed:** November 17, 2025  
**Status:** Complete  
**Next Action:** Try requesting a hypothesis generation document to see the fix in action!

