Update organic syn station.

Update docs
update "laiyu" missing init file. fix "laiyu" missing init file. fix "🐛 fix" 🐛 fix: config file is overwrited by default args even if not be set. mix 修改了mix，仿真流程报错问题
2025-12-15 13:44:39 +00:00 · 2025-12-15 02:34:36 +08:00 · 2025-12-14 13:13:21 +08:00
12 changed files with 95 additions and 109 deletions
--- a/README.md
+++ b/README.md
@@ -39,7 +39,9 @@ Uni-Lab-OS recommends using `mamba` for environment management. Choose the appro

 ```bash
 # Create new environment
-mamba create -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
+mamba create -n unilab python=3.11.11
+mamba activate unilab
+mamba install -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
 ```

 ## Install Dev Uni-Lab-OS
--- a/README_zh.md
+++ b/README_zh.md
@@ -41,7 +41,9 @@ Uni-Lab-OS 建议使用 `mamba` 管理环境。根据您的操作系统选择适

 ```bash
 # 创建新环境
-mamba create -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
+mamba create -n unilab python=3.11.11
+mamba activate unilab
+mamba install -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
 ```

 2. 安装开发版 Uni-Lab-OS:
--- a/docs/user_guide/installation.md
+++ b/docs/user_guide/installation.md
@@ -317,45 +317,6 @@ unilab --help

 如果所有命令都正常输出，说明开发环境配置成功！

-### 开发工具推荐
-
-#### IDE
-
- **PyCharm Professional**: 强大的 Python IDE，支持远程调试
- **VS Code**: 轻量级，配合 Python 扩展使用
- **Vim/Emacs**: 适合终端开发
-
-#### 推荐的 VS Code 扩展
-
- Python
- Pylance
- ROS
- URDF
- YAML
-
-#### 调试工具
-
-```bash
-# 安装调试工具
-pip install ipdb pytest pytest-cov -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
-
-# 代码质量检查
-pip install black flake8 mypy -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
-```
-
-### 设置 pre-commit 钩子（可选）
-
-```bash
-# 安装 pre-commit
-pip install pre-commit -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
-
-# 设置钩子
-pre-commit install
-
-# 手动运行检查
-pre-commit run --all-files
-```
-
 ---

 ## 验证安装
--- a/unilabos/app/main.py
+++ b/unilabos/app/main.py
@@ -159,9 +159,10 @@ def parse_args():
 def main():
    """主函数"""
    # 解析命令行参数
-    args = parse_args()
-    convert_argv_dashes_to_underscores(args)
-    args_dict = vars(args.parse_args())
+    parser = parse_args()
+    convert_argv_dashes_to_underscores(parser)
+    args = parser.parse_args()
+    args_dict = vars(args)

    # 环境检查 - 检查并自动安装必需的包 (可选)
    if not args_dict.get("skip_env_check", False):
@@ -220,17 +221,18 @@ def main():
        logger.info(f"Log level set to '{BasicConfig.log_level}' from config file.")
    configure_logger(loglevel=BasicConfig.log_level, working_dir=working_dir)

-    if args_dict["addr"] == "test":
-        print_status("使用测试环境地址", "info")
-        HTTPConfig.remote_addr = "https://uni-lab.test.bohrium.com/api/v1"
-    elif args_dict["addr"] == "uat":
-        print_status("使用uat环境地址", "info")
-        HTTPConfig.remote_addr = "https://uni-lab.uat.bohrium.com/api/v1"
-    elif args_dict["addr"] == "local":
-        print_status("使用本地环境地址", "info")
-        HTTPConfig.remote_addr = "http://127.0.0.1:48197/api/v1"
-    else:
-        HTTPConfig.remote_addr = args_dict.get("addr", "")
+    if args.addr != parser.get_default("addr"):
+        if args.addr == "test":
+            print_status("使用测试环境地址", "info")
+            HTTPConfig.remote_addr = "https://uni-lab.test.bohrium.com/api/v1"
+        elif args.addr == "uat":
+            print_status("使用uat环境地址", "info")
+            HTTPConfig.remote_addr = "https://uni-lab.uat.bohrium.com/api/v1"
+        elif args.addr == "local":
+            print_status("使用本地环境地址", "info")
+            HTTPConfig.remote_addr = "http://127.0.0.1:48197/api/v1"
+        else:
+            HTTPConfig.remote_addr = args.addr

    # 设置BasicConfig参数
    if args_dict.get("ak", ""):
@@ -327,6 +329,10 @@ def main():
    for ind, i in enumerate(resource_edge_info[::-1]):
        source_node: ResourceDict = nodes[i["source"]]
        target_node: ResourceDict = nodes[i["target"]]
+        if "sourceHandle" not in source_node:
+            continue
+        if "targetHandle" not in target_node:
+            continue
        source_handle = i["sourceHandle"]
        target_handle = i["targetHandle"]
        source_handler_keys = [
--- a/unilabos/config/config.py
+++ b/unilabos/config/config.py
@@ -41,7 +41,7 @@ class WSConfig:

 # HTTP配置
 class HTTPConfig:
-    remote_addr = "http://127.0.0.1:48197/api/v1"
+    remote_addr = "https://uni-lab.bohrium.com/api/v1"


 # ROS配置
--- a/unilabos/devices/laiyu_liquid_test/init.py
+++ b/unilabos/devices/laiyu_liquid_test/init.py
--- a/unilabos/devices/liquid_handling/laiyu/init.py
+++ b/unilabos/devices/liquid_handling/laiyu/init.py
--- a/unilabos/devices/liquid_handling/liquid_handler_abstract.py
+++ b/unilabos/devices/liquid_handling/liquid_handler_abstract.py
@@ -988,6 +988,18 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                dis_vols = [float(dis_vols)]
            else:
                dis_vols = [float(v) for v in dis_vols]
+
+        # 统一混合次数为标量，防止数组/列表与 int 比较时报错
+        if mix_times is not None and not isinstance(mix_times, (int, float)):
+            try:
+                mix_times = mix_times[0] if len(mix_times) > 0 else None
+            except Exception:
+                try:
+                    mix_times = next(iter(mix_times))
+                except Exception:
+                    pass
+        if mix_times is not None:
+            mix_times = int(mix_times)
            
            # 识别传输模式
            num_sources = len(sources)
--- a/unilabos/devices/liquid_handling/prcxi/prcxi.py
+++ b/unilabos/devices/liquid_handling/prcxi/prcxi.py
@@ -5,6 +5,7 @@ import json
 import os
 import socket
 import time
+import uuid
 from typing import Any, List, Dict, Optional, Tuple, TypedDict, Union, Sequence, Iterator, Literal

 from pylabrobot.liquid_handling import (
@@ -856,7 +857,30 @@ class PRCXI9300Api:

    def _raw_request(self, payload: str) -> str:
        if self.debug:
-            return " "
+            # 调试/仿真模式下直接返回可解析的模拟 JSON，避免后续 json.loads 报错
+            try:
+                req = json.loads(payload)
+                method = req.get("MethodName")
+            except Exception:
+                method = None
+
+            data: Any = True
+            if method in {"AddSolution"}:
+                data = str(uuid.uuid4())
+            elif method in {"AddWorkTabletMatrix", "AddWorkTabletMatrix2"}:
+                data = {"Success": True, "Message": "debug mock"}
+            elif method in {"GetErrorCode"}:
+                data = ""
+            elif method in {"RemoveErrorCodet", "Reset", "Start", "LoadSolution", "Pause", "Resume", "Stop"}:
+                data = True
+            elif method in {"GetStepStateList", "GetStepStatus", "GetStepState"}:
+                data = []
+            elif method in {"GetLocation"}:
+                data = {"X": 0, "Y": 0, "Z": 0}
+            elif method in {"GetResetStatus"}:
+                data = False
+
+            return json.dumps({"Success": True, "Msg": "debug mock", "Data": data})
        with contextlib.closing(socket.socket()) as sock:
            sock.settimeout(self.timeout)
            sock.connect((self.host, self.port))
--- a/unilabos/registry/devices/bioyond_dispensing_station.yaml
+++ b/unilabos/registry/devices/bioyond_dispensing_station.yaml
@@ -174,35 +174,6 @@ bioyond_dispensing_station:
          title: query_resource_by_name参数
          type: object
        type: UniLabJsonCommand
-      auto-transfer_materials_to_reaction_station:
-        feedback: {}
-        goal: {}
-        goal_default:
-          target_device_id: null
-          transfer_groups: null
-        handles: {}
-        placeholder_keys: {}
-        result: {}
-        schema:
-          description: ''
-          properties:
-            feedback: {}
-            goal:
-              properties:
-                target_device_id:
-                  type: string
-                transfer_groups:
-                  type: array
-              required:
-              - target_device_id
-              - transfer_groups
-              type: object
-            result: {}
-          required:
-          - goal
-          title: transfer_materials_to_reaction_station参数
-          type: object
-        type: UniLabJsonCommand
      auto-workflow_sample_locations:
        feedback: {}
        goal: {}
--- a/unilabos/resources/graphio.py
+++ b/unilabos/resources/graphio.py
@@ -284,10 +284,18 @@ def modify_to_backend_format(data: list[dict[str, Any]]) -> list[dict[str, Any]]
            edge["sourceHandle"] = port[source]
        elif "source_port" in edge:
            edge["sourceHandle"] = edge.pop("source_port")
+        else:
+            typ = edge.get("type")
+            if typ == "communication":
+                continue
        if target in port:
            edge["targetHandle"] = port[target]
        elif "target_port" in edge:
            edge["targetHandle"] = edge.pop("target_port")
+        else:
+            typ = edge.get("type")
+            if typ == "communication":
+                continue
        edge["id"] = f"reactflow__edge-{source}-{edge['sourceHandle']}-{target}-{edge['targetHandle']}"
        for key in ["source_port", "target_port"]:
            if key in edge:
--- a/unilabos/test/experiments/Grignard_flow_batchreact_single_pumpvalve.json
+++ b/unilabos/test/experiments/Grignard_flow_batchreact_single_pumpvalve.json
@@ -69,7 +69,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "device",
-            "class": "syringepump.runze",
+            "class": "syringe_pump_with_valve.runze.SY03B-T08",
            "position": {
                "x": 620.6111111111111,
                "y": 171,
@@ -93,7 +93,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 430.4087301587302,
                "y": 428,
@@ -117,7 +117,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 295.36944444444447,
                "y": 428,
@@ -141,7 +141,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 165.36944444444444,
                "y": 428,
@@ -165,7 +165,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 165.36944444444444,
                "y": 428,
@@ -189,7 +189,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 35,
                "y": 428,
@@ -213,7 +213,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 698.1111111111111,
                "y": 428,
@@ -255,7 +255,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "device",
-            "class": "syringepump.runze",
+            "class": "syringe_pump_with_valve.runze.SY03B-T08",
            "position": {
                "x": 1195.611507936508,
                "y": 686,
@@ -279,7 +279,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 1587.703373015873,
                "y": 1172.5,
@@ -299,7 +299,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "device",
-            "class": "separator_controller",
+            "class": "separator.homemade",
            "position": {
                "x": 1624.4027777777778,
                "y": 665.5,
@@ -320,7 +320,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 1614.404365079365,
                "y": 948,
@@ -340,7 +340,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 1915.7035714285714,
                "y": 665.5,
@@ -360,7 +360,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 1785.7035714285714,
                "y": 665.5,
@@ -384,7 +384,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 2054.0650793650793,
                "y": 665.5,
@@ -408,7 +408,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "device",
-            "class": "syringepump.runze",
+            "class": "syringe_pump_with_valve.runze.SY03B-T08",
            "position": {
                "x": 1630.6527777777778,
                "y": 448.5,
@@ -432,7 +432,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "device",
-            "class": "rotavap",
+            "class": "rotavap.one",
            "position": {
                "x": 1339.7031746031746,
                "y": 968.5,
@@ -453,7 +453,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 1339.7031746031746,
                "y": 1152,
@@ -473,7 +473,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 909.722619047619,
                "y": 948,
@@ -493,7 +493,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 867.972619047619,
                "y": 1152,
@@ -513,7 +513,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 742.722619047619,
                "y": 948,
@@ -533,7 +533,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 1206.722619047619,
                "y": 948,
@@ -553,7 +553,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "container",
-            "class": null,
+            "class": "container",
            "position": {
                "x": 1148.222619047619,
                "y": 1152,
@@ -573,7 +573,7 @@
            "children": [],
            "parent": "YugongStation",
            "type": "device",
-            "class": "syringepump.runze",
+            "class": "syringe_pump_with_valve.runze.SY03B-T08",
            "position": {
                "x": 1469.7031746031746,
                "y": 968.5,
Author	SHA1	Message	Date
Xuwznln	13a6795657	Update organic syn station.	2025-12-15 02:34:36 +08:00
Xianwei Qi	53219d8b04	Update docs update "laiyu" missing init file. fix "laiyu" missing init file. fix "🐛 fix" 🐛 fix: config file is overwrited by default args even if not be set. mix 修改了mix，仿真流程报错问题	2025-12-14 13:13:21 +08:00