科研项目结构初始化

项目文件夹/
├── 01_Scripts/
│   ├── 00_Templates/      # 脚本模板（Python + R）
│   │   ├── 01_Data_Cleaning.py
│   │   ├── 01_Data_Cleaning.R
│   │   ├── 02_Baseline_Table1.py
│   │   ├── 02_Baseline_Table1.R
│   │   ├── 03_Models_Survival_Reg.py
│   │   ├── 03_Models_Survival_Reg.R
│   │   └── ...
│   └── 99_Archive/        # 历史代码存档
├── 02_Input/              # 外部数据（只读）
├── 03_Results/
│   ├── 01_Final/          # 最终图表
│   ├── 02_Stages/         # 中间结果
│   └── 99_Archive/        # 结果存档
├── 04_Docs/               # 文档和日志
│   └── 99_Archive/
└── 项目名.Rproj           # RStudio工程文件

# 1. 替换为你自己的Python路径
PYTHON_EXEC="/Users/你的用户名/miniconda3/bin/python"

# 2. 调用Python脚本
"$PYTHON_EXEC" - "$@" <<'EOF'

import sys
import os
import subprocess
from pathlib import Path

# ================= 配置区域 =================

# 1. 文件夹结构列表
STRUCTURE_LIST = [
    "01_Scripts",
    "01_Scripts/00_Templates",
    "01_Scripts/99_Archive",
    "02_Input",
    "03_Results/01_Final",
    "03_Results/02_Stages",
    "03_Results/99_Archive",
    "04_Docs",
    "04_Docs/99_Archive",
]

# 2. 医学博士专用脚本模板名称
# 会同时生成Python (.py) 和R (.R) 版本
SCRIPT_BASENAMES = [
    "01_Data_Cleaning",        # 数据清洗
    "02_Baseline_Table1",      # 基线资料
    "03_Models_Survival_Reg",  # Cox/Logistic回归
    "04_Subgroup_Sensitivity", # 亚组分析
    "05_Plots_Visualization",  # 可视化
    "99_Utils_Config",        # 工具库
]

# ===========================================

def notify(title, message):
    safe_title = title.replace('"', '\\"')
    safe_message = message.replace('"', '\\"')
    os.system(f'osascript -e \'display notification "{safe_message}" with title "{safe_title}"\'')

def create_rproj_file(project_root):
    """创建RStudio项目文件"""
    try:
        rproj_name = f"{project_root.name}.Rproj"
        rproj_path = project_root / rproj_name

        content = """Version: 1.0

RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default

EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8

RnwWeave: Sweave
LaTeX: pdfLaTeX
"""
        if not rproj_path.exists():
            with open(rproj_path, 'w', encoding='utf-8') as f:
                f.write(content)
    except Exception:
        pass

def set_folder_view_settings(folder_path):
    """设置文件夹视图：列表、名称排序、展开"""
    try:
        p = str(folder_path.resolve())
        applescript = f'''
        tell application "Finder"
            try
                set target_folder to (POSIX file "{p}") as alias
                open target_folder
                tell container window of target_folder
                    set current view to list view
                    set sort column of list view options to name column
                    set sort direction of list view options to normal
                    try
                        set expanded of every folder of target_folder to true
                    end try
                end tell
                close container window of target_folder
            end try
        end tell
        '''
        subprocess.run(["osascript", "-e", applescript], check=False)
    except Exception:
        pass

def main():
    processed_count = 0

    for arg in sys.argv[1:]:
        target_root = Path(arg)

        # 确保是文件夹
        if not target_root.is_dir():
            target_root = target_root.parent

        try:
            # 步骤1: 创建文件夹结构
            for sub_path in STRUCTURE_LIST:
                full_path = target_root / sub_path
                full_path.mkdir(parents=True, exist_ok_ok=True)

            # 步骤2: 创建脚本模板
            templates_dir = target_root / "01_Scripts/00_Templates"
            if templates_dir.exists():
                for base_name in SCRIPT_BASENAMES:
                    for ext in [".py", ".R"]:
                        file_path = templates_dir / f"{base_name}{ext}"
                        if not file_path.exists():
                            file_path.touch()

            # 步骤3: 创建Rproj文件
            create_rproj_file(target_root)

            # 步骤4: 设置文件夹视图
            set_folder_view_settings(target_root)

            processed_count += 1

        except Exception as e:
            notify("创建出错", f"{target_root.name}: {str(e)}")

    if processed_count > 0:
        notify("项目初始化完成", f"已生成{processed_count}个项目的结构和模板")

if __name__ == "__main__":
    main()

EOF