Create 5 new protocols & bump version 0.9.8 (#59)

* 添加了5个缺失的protocol，验证了可以运行

* bump version to 0.9.8

* 修复新增的Action的字段缺失

---------

Co-authored-by: Xuwznln <18435084+Xuwznln@users.noreply.github.com>

unilabos/compile/recrystallize_protocol.py

@@ -0,0 +1,281 @@
+import networkx as nx
+from typing import List, Dict, Any, Tuple
+from .pump_protocol import generate_pump_protocol_with_rinsing
+
+
+def parse_ratio(ratio_str: str) -> Tuple[float, float]:
+    """
+    解析比例字符串，支持多种格式
+    
+    Args:
+        ratio_str: 比例字符串（如 "1:1", "3:7", "50:50"）
+    
+    Returns:
+        Tuple[float, float]: 比例元组 (ratio1, ratio2)
+    """
+    try:
+        # 处理 "1:1", "3:7", "50:50" 等格式
+        if ":" in ratio_str:
+            parts = ratio_str.split(":")
+            if len(parts) == 2:
+                ratio1 = float(parts[0])
+                ratio2 = float(parts[1])
+                return ratio1, ratio2
+        
+        # 处理 "1-1", "3-7" 等格式
+        if "-" in ratio_str:
+            parts = ratio_str.split("-")
+            if len(parts) == 2:
+                ratio1 = float(parts[0])
+                ratio2 = float(parts[1])
+                return ratio1, ratio2
+        
+        # 处理 "1,1", "3,7" 等格式
+        if "," in ratio_str:
+            parts = ratio_str.split(",")
+            if len(parts) == 2:
+                ratio1 = float(parts[0])
+                ratio2 = float(parts[1])
+                return ratio1, ratio2
+        
+        # 默认 1:1
+        print(f"RECRYSTALLIZE: 无法解析比例 '{ratio_str}'，使用默认比例 1:1")
+        return 1.0, 1.0
+    
+    except ValueError:
+        print(f"RECRYSTALLIZE: 比例解析错误 '{ratio_str}'，使用默认比例 1:1")
+        return 1.0, 1.0
+
+
+def find_solvent_vessel(G: nx.DiGraph, solvent: str) -> str:
+    """
+    查找溶剂容器
+    
+    Args:
+        G: 网络图
+        solvent: 溶剂名称
+    
+    Returns:
+        str: 溶剂容器ID
+    """
+    print(f"RECRYSTALLIZE: 正在查找溶剂 '{solvent}' 的容器...")
+    
+    # 构建可能的容器名称
+    possible_names = [
+        f"flask_{solvent}",
+        f"bottle_{solvent}",
+        f"reagent_{solvent}",
+        f"reagent_bottle_{solvent}",
+        f"{solvent}_flask",
+        f"{solvent}_bottle",
+        f"{solvent}",
+        f"vessel_{solvent}",
+    ]
+    
+    # 第一步：通过容器名称匹配
+    for vessel_name in possible_names:
+        if vessel_name in G.nodes():
+            print(f"RECRYSTALLIZE: 通过名称匹配找到容器: {vessel_name}")
+            return vessel_name
+    
+    # 第二步：通过模糊匹配
+    for node_id in G.nodes():
+        if G.nodes[node_id].get('type') == 'container':
+            node_name = G.nodes[node_id].get('name', '').lower()
+            
+            if solvent.lower() in node_id.lower() or solvent.lower() in node_name:
+                print(f"RECRYSTALLIZE: 通过模糊匹配找到容器: {node_id}")
+                return node_id
+    
+    # 第三步：通过液体类型匹配
+    for node_id in G.nodes():
+        if G.nodes[node_id].get('type') == 'container':
+            vessel_data = G.nodes[node_id].get('data', {})
+            liquids = vessel_data.get('liquid', [])
+            
+            for liquid in liquids:
+                if isinstance(liquid, dict):
+                    liquid_type = (liquid.get('liquid_type') or liquid.get('name', '')).lower()
+                    reagent_name = vessel_data.get('reagent_name', '').lower()
+                    
+                    if solvent.lower() in liquid_type or solvent.lower() in reagent_name:
+                        print(f"RECRYSTALLIZE: 通过液体类型匹配找到容器: {node_id}")
+                        return node_id
+    
+    raise ValueError(f"找不到溶剂 '{solvent}' 对应的容器")
+
+
+def generate_recrystallize_protocol(
+    G: nx.DiGraph,
+    ratio: str,
+    solvent1: str,
+    solvent2: str,
+    vessel: str,
+    volume: float,
+    **kwargs  # 接收其他可能的参数但不使用
+) -> List[Dict[str, Any]]:
+    """
+    生成重结晶协议序列
+    
+    Args:
+        G: 有向图，节点为容器和设备
+        ratio: 溶剂比例（如 "1:1", "3:7"）
+        solvent1: 第一种溶剂名称
+        solvent2: 第二种溶剂名称
+        vessel: 目标容器
+        volume: 总体积 (mL)
+        **kwargs: 其他可选参数，但不使用
+    
+    Returns:
+        List[Dict[str, Any]]: 动作序列
+    """
+    action_sequence = []
+    
+    print(f"RECRYSTALLIZE: 开始生成重结晶协议")
+    print(f"  - 比例: {ratio}")
+    print(f"  - 溶剂1: {solvent1}")
+    print(f"  - 溶剂2: {solvent2}")
+    print(f"  - 容器: {vessel}")
+    print(f"  - 总体积: {volume} mL")
+    
+    # 1. 验证目标容器存在
+    if vessel not in G.nodes():
+        raise ValueError(f"目标容器 '{vessel}' 不存在于系统中")
+    
+    # 2. 解析比例
+    ratio1, ratio2 = parse_ratio(ratio)
+    total_ratio = ratio1 + ratio2
+    
+    # 3. 计算各溶剂体积
+    volume1 = volume * (ratio1 / total_ratio)
+    volume2 = volume * (ratio2 / total_ratio)
+    
+    print(f"RECRYSTALLIZE: 解析比例: {ratio1}:{ratio2}")
+    print(f"RECRYSTALLIZE: {solvent1} 体积: {volume1:.2f} mL")
+    print(f"RECRYSTALLIZE: {solvent2} 体积: {volume2:.2f} mL")
+    
+    # 4. 查找溶剂容器
+    try:
+        solvent1_vessel = find_solvent_vessel(G, solvent1)
+        print(f"RECRYSTALLIZE: 找到溶剂1容器: {solvent1_vessel}")
+    except ValueError as e:
+        raise ValueError(f"无法找到溶剂1 '{solvent1}': {str(e)}")
+    
+    try:
+        solvent2_vessel = find_solvent_vessel(G, solvent2)
+        print(f"RECRYSTALLIZE: 找到溶剂2容器: {solvent2_vessel}")
+    except ValueError as e:
+        raise ValueError(f"无法找到溶剂2 '{solvent2}': {str(e)}")
+    
+    # 5. 验证路径存在
+    try:
+        path1 = nx.shortest_path(G, source=solvent1_vessel, target=vessel)
+        print(f"RECRYSTALLIZE: 溶剂1路径: {' → '.join(path1)}")
+    except nx.NetworkXNoPath:
+        raise ValueError(f"从溶剂1容器 '{solvent1_vessel}' 到目标容器 '{vessel}' 没有可用路径")
+    
+    try:
+        path2 = nx.shortest_path(G, source=solvent2_vessel, target=vessel)
+        print(f"RECRYSTALLIZE: 溶剂2路径: {' → '.join(path2)}")
+    except nx.NetworkXNoPath:
+        raise ValueError(f"从溶剂2容器 '{solvent2_vessel}' 到目标容器 '{vessel}' 没有可用路径")
+    
+    # 6. 添加第一种溶剂
+    print(f"RECRYSTALLIZE: 开始添加溶剂1 {volume1:.2f} mL")
+    
+    try:
+        pump_actions1 = generate_pump_protocol_with_rinsing(
+            G=G,
+            from_vessel=solvent1_vessel,
+            to_vessel=vessel,
+            volume=volume1,
+            amount="",
+            time=0.0,
+            viscous=False,
+            rinsing_solvent="",  # 重结晶不需要清洗
+            rinsing_volume=0.0,
+            rinsing_repeats=0,
+            solid=False,
+            flowrate=2.0,  # 正常流速
+            transfer_flowrate=0.5
+        )
+        
+        action_sequence.extend(pump_actions1)
+        
+    except Exception as e:
+        raise ValueError(f"生成溶剂1泵协议时出错: {str(e)}")
+    
+    # 7. 等待溶剂1稳定
+    action_sequence.append({
+        "action_name": "wait",
+        "action_kwargs": {
+            "time": 10.0,
+            "description": f"等待溶剂1 {solvent1} 稳定"
+        }
+    })
+    
+    # 8. 添加第二种溶剂
+    print(f"RECRYSTALLIZE: 开始添加溶剂2 {volume2:.2f} mL")
+    
+    try:
+        pump_actions2 = generate_pump_protocol_with_rinsing(
+            G=G,
+            from_vessel=solvent2_vessel,
+            to_vessel=vessel,
+            volume=volume2,
+            amount="",
+            time=0.0,
+            viscous=False,
+            rinsing_solvent="",  # 重结晶不需要清洗
+            rinsing_volume=0.0,
+            rinsing_repeats=0,
+            solid=False,
+            flowrate=2.0,  # 正常流速
+            transfer_flowrate=0.5
+        )
+        
+        action_sequence.extend(pump_actions2)
+        
+    except Exception as e:
+        raise ValueError(f"生成溶剂2泵协议时出错: {str(e)}")
+    
+    # 9. 等待溶剂2稳定
+    action_sequence.append({
+        "action_name": "wait",
+        "action_kwargs": {
+            "time": 10.0,
+            "description": f"等待溶剂2 {solvent2} 稳定"
+        }
+    })
+    
+    # 10. 等待重结晶完成
+    action_sequence.append({
+        "action_name": "wait",
+        "action_kwargs": {
+            "time": 600.0,  # 等待10分钟进行重结晶
+            "description": f"等待重结晶完成（{solvent1}:{solvent2} = {ratio}）"
+        }
+    })
+    
+    print(f"RECRYSTALLIZE: 协议生成完成，共 {len(action_sequence)} 个动作")
+    print(f"RECRYSTALLIZE: 预计总时间: {620/60:.1f} 分钟")
+    
+    return action_sequence
+
+
+# 测试函数
+def test_recrystallize_protocol():
+    """测试重结晶协议"""
+    print("=== RECRYSTALLIZE PROTOCOL 测试 ===")
+    
+    # 测试比例解析
+    test_ratios = ["1:1", "3:7", "50:50", "1-1", "2,8", "invalid"]
+    for ratio in test_ratios:
+        r1, r2 = parse_ratio(ratio)
+        print(f"比例 '{ratio}' -> {r1}:{r2}")
+    
+    print("测试完成")
+
+
+if __name__ == "__main__":
+    test_recrystallize_protocol()