Update workstation & bioyond example

Refine descriptions in Bioyond reaction station YAML

Updated and clarified field and operation descriptions in the reaction_station_bioyond.yaml file for improved accuracy and consistency. Changes include more precise terminology, clearer parameter explanations, and standardized formatting for operation schemas.

refactor(workstation): 更新反应站参数描述并添加分液站配置文件

修正反应站方法参数描述，使其更准确清晰
添加bioyond_dispensing_station.yaml配置文件

add create_workflow script and test

add invisible_slots to carriers

fix(warehouses): 修正bioyond_warehouse_1x4x4仓库的尺寸参数

调整仓库的num_items_x和num_items_z值以匹配实际布局，并更新物品尺寸参数

save resource get data. allow empty value for layout and cross_section_type

More decks&plates support for bioyond (#115)

refactor(registry): 重构反应站设备配置，简化并更新操作命令

移除旧的自动操作命令，新增针对具体化学操作的命令配置
更新模块路径和配置结构，优化参数定义和描述

fix(dispensing_station): 修正物料信息查询方法调用

将直接调用material_id_query改为通过hardware_interface调用，以符合接口设计规范

test/experiments/dispensing_station_bioyond.json

@@ -8,7 +8,7 @@
             ],
             "parent": null,
             "type": "device",
-            "class": "workstation.bioyond_dispensing_station",
+            "class": "bioyond_dispensing_station",
             "config": {
                 "config": {
                     "api_key": "DE9BDDA0",

test/workflow/example_bio.json

@@ -0,0 +1,186 @@
+{
+  "workflow": [
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_1",
+        "targets": "Liquid_2",
+        "asp_vol": 66.0,
+        "dis_vol": 66.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_2",
+        "targets": "Liquid_3",
+        "asp_vol": 58.0,
+        "dis_vol": 96.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_4",
+        "targets": "Liquid_2",
+        "asp_vol": 85.0,
+        "dis_vol": 170.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_4",
+        "targets": "Liquid_2",
+        "asp_vol": 63.333333333333336,
+        "dis_vol": 170.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_2",
+        "targets": "Liquid_3",
+        "asp_vol": 72.0,
+        "dis_vol": 150.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_4",
+        "targets": "Liquid_2",
+        "asp_vol": 85.0,
+        "dis_vol": 170.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_4",
+        "targets": "Liquid_2",
+        "asp_vol": 63.333333333333336,
+        "dis_vol": 170.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_2",
+        "targets": "Liquid_3",
+        "asp_vol": 72.0,
+        "dis_vol": 150.0,
+        "asp_flow_rate": 94.0,
+        "dis_flow_rate": 94.0
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_2",
+        "targets": "Liquid_3",
+        "asp_vol": 20.0,
+        "dis_vol": 20.0,
+        "asp_flow_rate": 7.6,
+        "dis_flow_rate": 7.6
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_5",
+        "targets": "Liquid_2",
+        "asp_vol": 6.0,
+        "dis_vol": 12.0,
+        "asp_flow_rate": 7.6,
+        "dis_flow_rate": 7.6
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_5",
+        "targets": "Liquid_2",
+        "asp_vol": 10.666666666666666,
+        "dis_vol": 12.0,
+        "asp_flow_rate": 7.599999999999999,
+        "dis_flow_rate": 7.6
+      }
+    },
+    {
+      "action": "transfer_liquid",
+      "action_args": {
+        "sources": "Liquid_2",
+        "targets": "Liquid_6",
+        "asp_vol": 12.0,
+        "dis_vol": 10.0,
+        "asp_flow_rate": 7.6,
+        "dis_flow_rate": 7.6
+      }
+    }
+  ],
+  "reagent": {
+    "Liquid_6": {
+      "slot": 1,
+      "well": [
+        "A2"
+      ],
+      "labware": "elution plate"
+    },
+    "Liquid_1": {
+      "slot": 2,
+      "well": [
+        "A1",
+        "A2",
+        "A4"
+      ],
+      "labware": "reagent reservoir"
+    },
+    "Liquid_4": {
+      "slot": 2,
+      "well": [
+        "A1",
+        "A2",
+        "A4"
+      ],
+      "labware": "reagent reservoir"
+    },
+    "Liquid_5": {
+      "slot": 2,
+      "well": [
+        "A1",
+        "A2",
+        "A4"
+      ],
+      "labware": "reagent reservoir"
+    },
+    "Liquid_2": {
+      "slot": 4,
+      "well": [
+        "A2"
+      ],
+      "labware": "TAG1 plate on Magnetic Module GEN2"
+    },
+    "Liquid_3": {
+      "slot": 12,
+      "well": [
+        "A1"
+      ],
+      "labware": "Opentrons Fixed Trash"
+    }
+  }
+}

test/workflow/merge_workflow.py

@@ -0,0 +1,14 @@
+import pytest
+import json
+from scripts.workflow import build_protocol_graph, draw_protocol_graph, draw_protocol_graph_with_ports
+
+
+@pytest.mark.parametrize("protocol_name", [
+    "example_bio",
+    # "bioyond_materials_liquidhandling_1",
+])
+def test_build_protocol_graph(protocol_name):
+    d = json.load(open(f"{protocol_name}.json"))
+    graph = build_protocol_graph(labware_info=d["reagent"], protocol_steps=d["workflow"], workstation_name="PRCXi")
+    draw_protocol_graph_with_ports(graph, "graph.png")
+    print(graph)