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https://github.com/dptech-corp/Uni-Lab-OS.git
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modify workstation_architecture docs bioyond_HR (#133) * feat: Enhance Bioyond synchronization and resource management - Implemented synchronization for all material types (consumables, samples, reagents) from Bioyond, logging detailed information for each type. - Improved error handling and logging during synchronization processes. - Added functionality to save Bioyond material IDs in UniLab resources for future updates. - Enhanced the `sync_to_external` method to handle material movements correctly, including querying and creating materials in Bioyond. - Updated warehouse configurations to support new storage types and improved layout for better resource management. - Introduced new resource types such as reactors and tip boxes, with detailed specifications. - Modified warehouse factory to support column offsets for naming conventions (e.g., A05-D08). - Improved resource tracking by merging extra attributes instead of overwriting them. - Added a new method for updating resources in Bioyond, ensuring better synchronization of resource changes. * feat: 添加TipBox和Reactor的配置到bottles.yaml * fix: 修复液体投料方法中的volume参数处理逻辑 修复solid_feeding_vials方法中的volume参数处理逻辑,优化solvents参数的使用条件 更新液体投料方法,支持通过溶剂信息自动计算体积,添加solvents参数并更新文档描述 Add batch creation methods for vial and solution tasks 添加批量创建90%10%小瓶投料任务和二胺溶液配置任务的功能,更新相关参数和默认值
211 lines
6.7 KiB
Python
211 lines
6.7 KiB
Python
# Configuration file for the Sphinx documentation builder.
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# Sphinx 文档生成器的配置文件
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# For the full list of built-in configuration values, see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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import os
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import sys
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# 将项目的根目录添加到 sys.path 中,以便 Sphinx 能够找到 unilabos 包
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sys.path.insert(0, os.path.abspath(".."))
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project = "Uni-Lab"
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copyright = "2025, Uni-Lab Community, DP Technology & Peking University"
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author = "Uni-Lab Community, DP Technology & Peking University"
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# -- General configuration ---------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
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extensions = [
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"myst_parser",
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"sphinx.ext.autodoc",
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"sphinx.ext.napoleon", # 如果您使用 Google 或 NumPy 风格的 docstrings
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"sphinx_rtd_theme",
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"sphinxcontrib.mermaid"
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]
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source_suffix = {
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".rst": "restructuredtext",
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".txt": "markdown",
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".md": "markdown",
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}
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myst_enable_extensions = [
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"colon_fence",
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"deflist",
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"dollarmath",
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"html_image",
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"replacements",
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"smartquotes",
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"substitution",
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]
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myst_fence_as_directive = ["mermaid"]
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templates_path = ["_templates"]
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exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
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language = "zh"
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# -- Options for HTML output -------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
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# 设置 HTML 主题为 sphinx-book-theme
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html_theme = "sphinx_rtd_theme"
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# sphinx-book-theme 主题选项
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html_theme_options = {
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"repository_url": "https://github.com/用户名/Uni-Lab",
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"use_repository_button": True,
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"use_issues_button": True,
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"use_edit_page_button": True,
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"use_download_button": True,
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"path_to_docs": "docs",
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"show_navbar_depth": 2,
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"show_toc_level": 2,
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"home_page_in_toc": True,
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"logo_only": False,
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}
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# 设置 HTML 文档的静态文件路径
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html_static_path = ["_static"] # 如果有自定义 CSS,可以放在 _static 目录中
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section_titles = {
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"Simple": "## 简单单变量动作函数",
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"Organic": """## 常量有机化学操作
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Uni-Lab 常量有机化学指令集多数来自 [XDL](https://croningroup.gitlab.io/chemputer/xdl/standard/full_steps_specification.html#),包含有机合成实验中常见的操作,如加热、搅拌、冷却等。
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""",
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"Bio": """## 移液工作站及相关生物自动化设备操作
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Uni-Lab 生物操作指令集多数来自 [PyLabRobot](https://docs.pylabrobot.org/user_guide/index.html),包含生物实验中常见的操作,如移液、混匀、离心等。
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""",
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"MobileRobot": "## 多工作站及小车运行、物料转移",
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"Robot": """## 机械臂、夹爪等机器人设备
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Uni-Lab 机械臂、机器人、夹爪和导航指令集沿用 ROS2 的 `control_msgs` 和 `nav2_msgs`:
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""",
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}
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import os
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from pathlib import Path
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def get_conda_share_dir(package_name=None):
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"""获取 Conda 环境的 share 目录路径
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:param package_name: 可选参数,指定具体包的 share 子目录
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:return: Path 对象或 None
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"""
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# 获取当前 Conda 环境根目录
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conda_prefix = os.getenv("CONDA_PREFIX")
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if not conda_prefix:
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raise EnvironmentError("未检测到激活的 Conda 环境")
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# 构建基础 share 目录路径
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share_dir = Path(conda_prefix) / "share"
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# 如果指定了包名,追加包子目录
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if package_name:
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share_dir = share_dir / package_name
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# 验证路径是否存在
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if not share_dir.exists():
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print(f"警告: 路径 {share_dir} 不存在")
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return None
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return share_dir
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def generate_action_includes(app):
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src_dir = Path(app.srcdir)
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print(f"Generating action includes for {src_dir}")
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action_dir = src_dir.parent / "unilabos_msgs" / "action" # 修改为你的实际路径
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output_file = src_dir / "developer_guide" / "action_includes.md"
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# 确保输出目录存在
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output_file.parent.mkdir(exist_ok=True)
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# 初始化各部分内容
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sections = {}
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# 仅处理本地消息文件
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if action_dir.exists():
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for action_file in sorted(action_dir.glob("*.action")):
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# 获取相对路径
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rel_path = f"../../unilabos_msgs/action/{action_file.name}"
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# 读取首行注释
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try:
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with open(action_file, "r", encoding="utf-8") as af:
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first_line = af.readline().strip()
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# 提取注释内容(去除#和空格)
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section = first_line.lstrip("#").strip()
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text = f"""
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### `{action_file.stem}`
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```{{literalinclude}} {rel_path}
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:language: yaml
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```
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----
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"""
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if sections.get(section) is None:
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sections[section] = text
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else:
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sections[section] += text
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except Exception as e:
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print(f"处理文件 {action_file} 时出错: {e}")
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else:
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print(f"警告: 动作消息目录 {action_dir} 不存在")
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ros_action_dirs = []
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control_msgs_dir = get_conda_share_dir("control_msgs")
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nav2_msgs_dir = get_conda_share_dir("nav2_msgs")
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if control_msgs_dir is not None:
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ros_action_dirs.append(control_msgs_dir / "action")
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if nav2_msgs_dir is not None:
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ros_action_dirs.append(nav2_msgs_dir / "action")
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for action_dir in ros_action_dirs:
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for action_file in sorted(action_dir.glob("*.action")):
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# 获取相对路径
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rel_path = f"{action_file.absolute()}"
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# 读取首行注释
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with open(action_file, "r", encoding="utf-8") as af:
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# 提取注释内容(去除#和空格)
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section = "Robot"
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text = f"""### `{action_file.stem}`
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```yaml
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{open(rel_path, 'r').read()}
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```
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----
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"""
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if sections.get(section) is None:
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sections[section] = text
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else:
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sections[section] += text
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# 写入内容到输出文件
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with open(output_file, "w", encoding="utf-8") as f:
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# 按 Section 生成总文档
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for section, title in section_titles.items():
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content = sections.get(section, "")
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if content: # 只有有内容时才写入标题和内容
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f.write(f"{title}\n\n")
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f.write(content)
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def setup(app):
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app.connect("builder-inited", generate_action_includes)
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app.add_js_file("https://cdn.jsdelivr.net/npm/mermaid/dist/mermaid.min.js")
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app.add_js_file(None, body="mermaid.initialize({startOnLoad:true});")
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