# 🎉 BioQL VS Code Extension v3.3.1 - FINAL

**Date**: October 2, 2025
**Status**: ✅ **PRODUCTION READY WITH REASONING DISPLAY**

---

## 🔧 Cambios en v3.3.1

### Problema Identificado
El chat participant (`@bioql`) mostraba el código de forma incorrecta. El servidor retornaba:
```json
{
  "code": "from bioql import quantum\n\nresult = quantum(...)",
  "reasoning": "Bell state is a maximally entangled 2-qubit state..."
}
```

Pero la extensión solo mostraba `result.code` sin formato, causando output mal formateado.

### Solución Implementada

1. **Nueva función `callBioQLAssistantFull()`**
   - Retorna objeto con `{code, reasoning}`
   - Mantiene compatibilidad con función original
   - Agrega `include_reasoning: true` al request

2. **Chat participant mejorado**
   - Muestra reasoning en sección separada
   - Código en bloque markdown formateado
   - Agrega trigger para "revisa" (español)
   - Botón "Insert Code" solo inserta código (no reasoning)

3. **Output mejorado**
   ```markdown
   ### Reasoning

   Bell state is a maximally entangled 2-qubit state. Steps: 1) Apply Hadamard to qubit 0...

   ### Code

   ```python
   from bioql import quantum

   result = quantum("Create Bell state", backend="simulator", shots=1024)
   print(result)
   ```
   ```

---

## 📦 Archivos Actualizados

### `/vscode-extension/extension.js`

**Cambios**:
1. Nueva función `callBioQLAssistantFull()` (línea 380-462)
2. `handleChatRequest()` actualizado para usar reasoning (línea 261-329)
3. Agrega "revisa" como trigger palabra (línea 274)
4. Muestra reasoning y code separadamente (línea 279-284)
5. Log mejorado en Output panel con nombre del modelo (línea 420)

**Funciones clave**:
```javascript
async function callBioQLAssistantFull(prompt, mode) {
    // ...
    return {
        code: result.code || '',
        reasoning: result.reasoning || ''
    };
}

async function handleChatRequest(request, context, stream, token) {
    const result = await callBioQLAssistantFull(prompt, mode);

    if (result.reasoning) {
        stream.markdown('### Reasoning\n\n' + result.reasoning + '\n\n');
    }

    stream.markdown('### Code\n\n```python\n' + result.code + '\n```\n\n');

    stream.button({
        command: 'bioql.insertCode',
        title: 'Insert Code',
        arguments: [result.code]  // Solo código, no reasoning
    });
}
```

### `/vscode-extension/package.json`

**Cambios**:
- Version: `3.3.0` → `3.3.1`
- Description: Updated to mention fine-tuned DeepSeek model
- Default mode: `template` → `modal`
- Default modalUrl: Updated to DeepSeek endpoint

---

## 🎯 Funcionalidades

### 1. Chat Participant (@bioql)

**Triggers para generación de código**:
- "generate" → Genera código
- "create" → Genera código
- "write" → Genera código
- "revisa" → Revisa y genera código (español) ✨ NEW

**Output format**:
```
### Reasoning

[Explicación paso a paso del algoritmo cuántico]

### Code

```python
[Código BioQL válido]
```

[Insert Code] ← Botón para insertar
```

### 2. Commands

- `Cmd/Ctrl+Shift+G`: Generate Code
- `Cmd/Ctrl+Shift+F`: Fix Code
- Chat: Type `@bioql` followed by request

### 3. Cost Tracking

Output panel muestra:
```
🔄 Calling BioQL inference API...
   Endpoint: https://spectrix--bioql-inference-deepseek-generate-code.modal.run

💰 Cost Information:
   Model: deepseek-coder-1.3b-bioql-finetuned
   User Cost: $0.002279
   Generation Time: 5.328s
   Profit Margin: 40.0%
   Balance: $9.987070
```

---

## 🧪 Testing

### Test 1: Generación Simple
**Input (Chat)**: `@bioql create a Bell state`

**Expected Output**:
```
### Reasoning

Bell state is a maximally entangled 2-qubit state. Steps: 1) Apply Hadamard to qubit 0 to create superposition, 2) Apply CNOT with qubit 0 as control and qubit 1 as target to create entanglement.

### Code

```python
from bioql import quantum

result = quantum("Create Bell state", backend="simulator", shots=1024)
print(result)
```

[Insert Code]
```

### Test 2: Revisión de Código (Español)
**Input (Chat)**: `@bioql revisa mi codigo en /Users/heinzjungbluth/Test/clinical_study.py`

**Expected Output**:
- Muestra reasoning sobre qué agregar/mejorar
- Genera código BioQL sugerido
- Botón para insertar código

### Test 3: Command Shortcut
**Input**: `Cmd+Shift+G` → Type "Create 3-qubit GHZ state"

**Expected**:
- Código insertado directamente en editor
- Output panel muestra costos
- No muestra reasoning en editor (solo en output panel si es relevante)

---

## 📊 Comparación de Versiones

| Feature | v3.2.0 | v3.3.0 | v3.3.1 |
|---------|--------|--------|--------|
| Model | CodeLlama-7B | DeepSeek fine-tuned | DeepSeek fine-tuned |
| Reasoning | ❌ No | ✅ Backend | ✅ Backend + Display |
| Chat Display | Plain text | Code block only | Reasoning + Code |
| Español Support | ❌ No | ❌ No | ✅ "revisa" trigger |
| Format Quality | Poor | Good | Excellent |
| Default Mode | `template` | `modal` | `modal` |

---

## 🚀 Installation

### From VSIX
```bash
code --install-extension bioql-assistant-3.3.1.vsix
```

### Configuration
```json
{
  "bioql.mode": "modal",
  "bioql.apiKey": "bioql_test_870ce7ae",
  "bioql.modalUrl": "https://spectrix--bioql-inference-deepseek-generate-code.modal.run"
}
```

---

## 🐛 Issues Fixed

### Issue 1: Malformed Chat Output ✅
**Before**:
```
bioql
from bioql import quantum

result = quantum("H", 0) - print("Result:", result)

if result == 0:

print("Result: 0")
```

**After**:
```
### Reasoning

To apply Hadamard gate to qubit 0, we use the quantum() function...

### Code

```python
from bioql import quantum

result = quantum("Apply H gate to qubit 0", backend="simulator", shots=1024)
print("Result:", result)
```
```

### Issue 2: Reasoning Not Displayed ✅
**Before**: Only code shown, reasoning discarded
**After**: Reasoning shown in separate section before code

### Issue 3: Wrong Function Called ✅
**Before**: `callBioQLAssistant()` only returned code string
**After**: `callBioQLAssistantFull()` returns `{code, reasoning}` object

---

## 📝 Code Changes Summary

### New Functions
1. `callBioQLAssistantFull(prompt, mode)` - Returns full response
2. Updated `handleChatRequest()` - Shows reasoning and code separately

### Modified Functions
1. `callBioQLAssistant()` - Now wrapper around `callBioQLAssistantFull()`
2. Chat triggers - Added "revisa" for Spanish support

### API Changes
- Added `include_reasoning: true` to Modal API requests
- Response parsing handles both `code` and `reasoning` fields
- Output channel logs model name

---

## 🎯 Production Checklist

- [x] Model deployed (DeepSeek fine-tuned)
- [x] Extension updated to show reasoning
- [x] Chat formatting fixed
- [x] Spanish trigger added ("revisa")
- [x] Cost tracking working
- [x] Insert Code button working
- [x] Output panel logs complete
- [x] Package created (v3.3.1)
- [x] Testing completed
- [x] Documentation updated

---

## 📁 Files

**Extension Package**: `bioql-assistant-3.3.1.vsix` (856 KB)

**Source Files**:
- `/vscode-extension/extension.js` - Main logic
- `/vscode-extension/package.json` - Metadata

**Model Endpoint**:
- `https://spectrix--bioql-inference-deepseek-generate-code.modal.run`

**Demo API Key**:
- `bioql_test_870ce7ae`

---

## ✅ Status: PRODUCTION READY

**Sistema completamente funcional**:
- ✅ Modelo DeepSeek fine-tuned deployado
- ✅ Reasoning display implementado
- ✅ Chat formatting correcto
- ✅ Código BioQL válido generado
- ✅ Soporte español agregado
- ✅ Cost tracking funcionando
- ✅ Extension empaquetada y lista

**To Install**:
```bash
cd /Users/heinzjungbluth/Desktop/bioql/vscode-extension
code --install-extension bioql-assistant-3.3.1.vsix
```

**To Configure**:
1. Open VS Code Settings (`Cmd/Ctrl+,`)
2. Search "bioql"
3. Set API key: `bioql_test_870ce7ae`
4. Mode should be: `modal` (default)
5. URL should be: DeepSeek endpoint (default)

**To Test**:
1. Open any `.py` file
2. Type `@bioql create a Bell state` in chat
3. Verify reasoning and code are shown separately
4. Click "Insert Code" button
5. Check Output panel for costs

---

**Date**: October 2, 2025
**Version**: 3.3.1
**Status**: ✅ **READY FOR USE**
