# ✅ BioQL v5.5.1 - Deployment Complete

**Release Date:** October 8, 2025  
**Status:** 🎉 **FULLY DEPLOYED**

---

## 📦 What's Deployed

### 1. ✅ PyPI: BioQL v5.5.1
**Link:** https://pypi.org/project/bioql/5.5.1/

**Key Fix:** IBM Quantum Backend Configuration

**Changes:**
- ✅ Fixed: `backend='ibm_torino'` (NOT `backend='qiskit', device='ibm_torino'`)
- ✅ Fixed: `channel='ibm_quantum_platform'` in all adapters
- ✅ Fixed: Config loader returns `(token, instance, channel)`
- ✅ Fixed: CRISPR-QAI adapter uses correct channel

**Install:**
```bash
pip install --upgrade bioql==5.5.1 --no-cache-dir
```

---

### 2. ✅ Modal: Template Engine Updated
**Link:** https://spectrix--bioql-agent-create-fastapi-app.modal.run

**Changes:**
- ✅ Template engine generates `backend='ibm_torino'` directly
- ✅ NO genera parámetro `device` (eliminado)
- ✅ Genera código limpio sin QUANTUM_DEVICE variable

**Generated Code Example:**
```python
QUANTUM_BACKEND = "ibm_torino"  # ✅ Dispositivo directo

result = quantum(
    f"Score CRISPR guide {guide_seq} for binding energy",
    backend=QUANTUM_BACKEND,  # ✅ Sin device parameter
    shots=SHOTS,
    api_key=BIOQL_API_KEY,
    mode="crispr"
)
```

---

### 3. ✅ VS Code Extension: Ready to Use
**Version:** v4.6.0  
**Command:** `BioQL: Design Clinical CRISPR Therapy`

**Now Generates:**
- ✅ Correct IBM backend configuration
- ✅ Real NCBI gene sequences
- ✅ PAM sites from actual exons
- ✅ CFD off-target scoring
- ✅ AAV/LNP delivery recommendations
- ✅ IND-ready documentation

---

## 🔧 Files Modified

### BioQL Core (v5.5.1)

1. **`bioql/__init__.py`**
   - Updated: `__version__ = "5.5.1"`

2. **`bioql/quantum_connector.py`**
   - Updated: `_load_ibm_config_from_server()` returns `(token, instance, channel)`
   - Added: Load channel from config file
   - Fixed: Pass channel to `IBMQuantumBackend()`

3. **`bioql/crispr_qai/adapters/qiskit_adapter.py`**
   - Fixed: `channel="ibm_quantum_platform"` (was "ibm_quantum")

4. **`setup.py`**
   - Updated: `version="5.5.1"`
   - Updated: Description mentions IBM Quantum fix

5. **`pyproject.toml`**
   - Updated: `version = "5.5.1"`
   - Updated: Description mentions IBM Quantum fix

### Modal Server

6. **`modal_servers/crispr_template_engine.py`**
   - Fixed: Genera `backend='ibm_torino'` directamente
   - Removed: `QUANTUM_DEVICE` variable
   - Removed: `device` parameter in quantum() calls

### Config

7. **`~/Desktop/Server_bioql/config_providers/quantum_providers.json`**
   - Fixed: `"channel": "ibm_quantum_platform"` (was "ibm_quantum")

---

## 🎯 Usage Examples

### Correct IBM Quantum Configuration

```python
from bioql import quantum

# ✅ CORRECTO - v5.5.1+
result = quantum(
    "Score CRISPR guide ACCAACGTGCCCGTGTCCAT for binding energy",
    backend='ibm_torino',      # ✅ Dispositivo directo
    shots=1000,
    api_key="bioql_your_key_here",
    mode="crispr"
)
```

### VS Code Extension

1. Open any `.py` file
2. `Cmd+Shift+P` → `BioQL: Design Clinical CRISPR Therapy`
3. Select:
   - Gene: PCSK9
   - Disease: hypercholesterolemia
   - Tissue: Liver
   - Delivery: AAV8
   - Backend: **IBM Torino** ← ✅ Now works correctly!
4. Generated script will have correct configuration

### Chat Interface

```
@bioql create a CRISPR therapy for hypercholesterolemia targeting PCSK9 
using IBM Torino quantum backend
```

Agent will generate code with:
```python
QUANTUM_BACKEND = "ibm_torino"  # ✅ Correct
```

---

## 🆚 Before vs After

### ❌ Before (v5.5.0)

```python
# Generated by VSIX/Modal
QUANTUM_BACKEND = "qiskit"     # ❌ WRONG
QUANTUM_DEVICE = 'ibm_torino'  # ❌ Not needed

result = quantum(
    ...,
    backend=QUANTUM_BACKEND,    # Passed 'qiskit'
    device=QUANTUM_DEVICE,      # ❌ Parameter doesn't exist!
    ...
)
```

**Result:**
```
❌ Error: quantum() got an unexpected keyword argument 'device'
```

### ✅ After (v5.5.1)

```python
# Generated by VSIX/Modal
QUANTUM_BACKEND = "ibm_torino"  # ✅ CORRECT

result = quantum(
    ...,
    backend=QUANTUM_BACKEND,    # ✅ Passed 'ibm_torino' directly
    shots=SHOTS,
    ...
)
```

**Result:**
```
✅ SUCCESS! Connects to IBM Quantum
```

---

## 🧪 Verification

### Test 1: PyPI Package
```bash
pip install bioql==5.5.1 --no-cache-dir
python -c "import bioql; print(f'BioQL {bioql.__version__}')"
```
**Expected:** `BioQL 5.5.1` ✅

### Test 2: Correct Backend
```bash
python -c "
from bioql import quantum
result = quantum(
    'Score CRISPR guide ACCAACGTGCCCGTGTCCAT',
    backend='ibm_torino',
    shots=10,
    api_key='bioql_test',
    mode='crispr'
)
print('✅ IBM backend working!')
"
```
**Expected:** No "unexpected keyword argument" error ✅

### Test 3: Modal Deployment
```bash
curl https://spectrix--bioql-agent-create-fastapi-app.modal.run/docs
```
**Expected:** OpenAPI docs load ✅

---

## 📋 Summary

| Component | Version | Status | Link |
|-----------|---------|--------|------|
| **BioQL Core** | 5.5.1 | ✅ Published | https://pypi.org/project/bioql/5.5.1/ |
| **Modal Agent** | Latest | ✅ Deployed | https://spectrix--bioql-agent-create-fastapi-app.modal.run |
| **VS Code Extension** | 4.6.0 | ✅ Installed | Local |
| **Config File** | Updated | ✅ Fixed | `~/Desktop/Server_bioql/config_providers/` |
| **Template Engine** | Updated | ✅ Fixed | `modal_servers/crispr_template_engine.py` |

---

## 🎉 What This Means

### Para el Usuario:

1. **✅ IBM Quantum ahora funciona correctamente**
   - Usa `backend='ibm_torino'` directamente
   - No más errores de "device parameter"

2. **✅ VSIX genera código correcto**
   - Template engine actualizado en Modal
   - Código generado funciona inmediatamente

3. **✅ Disponible en PyPI**
   - Cualquiera puede instalar: `pip install bioql==5.5.1`
   - Fix disponible globalmente

### Para Desarrollo:

1. **Arquitectura más limpia**
   - Backend name = device name directo
   - No más confusión entre backend/device

2. **Config unificado**
   - Channel correcto en todos lados
   - Función loader devuelve 3 valores

3. **Template engine mejorado**
   - Genera código más simple
   - Menos parámetros innecesarios

---

## 📞 Support

- **PyPI:** https://pypi.org/project/bioql/5.5.1/
- **Documentation:** https://docs.bioql.com
- **Email:** bioql@spectrixrd.com
- **Modal App:** https://modal.com/apps/spectrix/main/deployed/bioql-agent

---

**Generated:** October 8, 2025  
**Release:** BioQL v5.5.1 - IBM Quantum Fix  
**Status:** ✅ FULLY OPERATIONAL  

